I tried adding a subfolder to all the root folder to see if that helped. Unfortunately, it did not.
Jun 07, 2019 11:54:58.885 [5748] INFO - Plex Media Scanner v1.15.8.1163-005053bb5 - Microsoft PC x64 - build: windows-x86 - GMT 02:00
Jun 07, 2019 11:54:58.885 [5748] INFO - Windows version: 6.2 (Build 9200), language en-US
Jun 07, 2019 11:54:58.886 [5748] INFO - 8 3696 MHz processor(s): Architecture=0, Level=6, Revision=40458 Processor Identifier=Intel64 Family 6 Model 158 Stepping 10, GenuineIntel
Jun 07, 2019 11:54:58.886 [5748] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 14 --directory "X:\Movies2160\Z\Zero Dark Thirty (2012) [tt1790885]"
Jun 07, 2019 11:54:58.883 [2492] VERBOSE - [FFMPEG] - Rescanning for external libs: 'C\:\\Users\\aj\\AppData\\Local\\Plex\ Media\ Server\\Codecs\\392df4f-2292-windows-x86\\'
Jun 07, 2019 11:54:58.883 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\aac_decoder.dll
Jun 07, 2019 11:54:58.884 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\ac3_decoder.dll
Jun 07, 2019 11:54:58.884 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\dca_decoder.dll
Jun 07, 2019 11:54:58.885 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\h264_decoder.dll
Jun 07, 2019 11:54:58.885 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\hevc_decoder.dll
Jun 07, 2019 11:54:58.885 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\libx264_encoder.dll
Jun 07, 2019 11:54:58.886 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg1video_decoder.dll
Jun 07, 2019 11:54:58.886 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg2video_decoder.dll
Jun 07, 2019 11:54:58.887 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg4_decoder.dll
Jun 07, 2019 11:54:58.887 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\msmpeg4v1_decoder.dll
Jun 07, 2019 11:54:58.887 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\msmpeg4v3_decoder.dll
Jun 07, 2019 11:54:58.888 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\vc1_decoder.dll
Jun 07, 2019 11:54:58.888 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\vp9_decoder.dll
Jun 07, 2019 11:54:58.888 [2492] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\wmv3_decoder.dll
Jun 07, 2019 11:54:58.889 [2492] DEBUG - Opening 20 database sessions to library (com.plexapp.plugins.library), SQLite 3.26.0, threadsafe=1
Jun 07, 2019 11:54:58.997 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:03.779 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:08.545 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:13.304 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:17.614 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:21.894 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:26.187 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:30.539 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:34.962 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:39.366 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:43.694 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:55:48.141 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:52.558 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:55:55.607 [2492] DEBUG - It took 62.500000 ms to retrieve 0 items.
Jun 07, 2019 11:55:56.929 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:01.337 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:05.756 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:10.086 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:14.477 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:18.821 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:23.192 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:27.537 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:31.947 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:56:36.289 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:40.683 [2492] DEBUG - It took 15.625000 ms to retrieve 533 items.
Jun 07, 2019 11:56:45.022 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:49.413 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:53.771 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:56:58.133 [2492] DEBUG - It took 0.000000 ms to retrieve 533 items.
Jun 07, 2019 11:57:02.547 [2492] DEBUG - Scanning [Cloud] Movies (2160p) using en(Plex Movie Scanner) with 1 current media items and 1 section locations in the database...
Jun 07, 2019 11:57:02.547 [5808] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/notify/cullTimeline?librarySectionID=14&sinceTime=1559900222
Jun 07, 2019 11:57:02.550 [5808] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/notify/cullTimeline?librarySectionID=14&sinceTime=1559900222
Jun 07, 2019 11:57:02.597 [2492] DEBUG - Performing a scan with 'Plex Movie Scanner' (language: en virtual: 0).
Jun 07, 2019 11:57:02.597 [2492] DEBUG - * Scanning X:\Movies2160\Z\Zero Dark Thirty (2012) [tt1790885]
Jun 07, 2019 11:57:02.597 [2492] DEBUG - * Scanning directory X:\Movies2160\Z\Zero Dark Thirty (2012) [tt1790885] (parent: yes)
Jun 07, 2019 11:57:02.597 [2492] VERBOSE - * Noting that 'Zero Dark Thirty (2012) [tt1790885]' was updated at 2019-05-10 23:29:33
Jun 07, 2019 11:57:02.597 [2492] VERBOSE - * Taking directory 'Zero Dark Thirty (2012) [tt1790885]' (45906) out of the map (0 left)
Jun 07, 2019 11:57:02.598 [2492] DEBUG - Adding file for scanner: "X:\Movies2160\Z\Zero Dark Thirty (2012) [tt1790885]\Zero.Dark.Thirty.2012.2160p.BluRay.REMUX.HEVC.DTS-HD.MA.TrueHD.7.1.Atmos-FGT.mkv"
Jun 07, 2019 11:57:02.602 [2492] DEBUG - Skipping over directory 'Zero Dark Thirty (2012) [tt1790885]', as nothing has changed; removing 1 media items from map.
Jun 07, 2019 11:57:02.606 [5808] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Zero%20Dark%20Thirty%20(2012)%20[tt1790885]
Jun 07, 2019 11:57:02.610 [2492] DEBUG - Removing 0 media items that were left.
Jun 07, 2019 11:57:02.610 [2492] DEBUG - Removing 0 directories that were left.
Jun 07, 2019 11:57:02.611 [2492] DEBUG - Refreshing section 14 of type: 1
Jun 07, 2019 11:57:02.613 [2484] DEBUG - Refreshing 0 IDs.
Jun 07, 2019 11:57:02.617 [5808] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Zero%20Dark%20Thirty%20(2012)%20[tt1790885]
Jun 07, 2019 12:54:00.927 [6724] INFO - Plex Media Scanner v1.15.8.1163-005053bb5 - Microsoft PC x64 - build: windows-x86 - GMT 02:00
Jun 07, 2019 12:54:00.928 [6724] INFO - Windows version: 6.2 (Build 9200), language en-US
Jun 07, 2019 12:54:00.928 [6724] INFO - 8 3696 MHz processor(s): Architecture=0, Level=6, Revision=40458 Processor Identifier=Intel64 Family 6 Model 158 Stepping 10, GenuineIntel
Jun 07, 2019 12:54:00.928 [6724] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 14 --directory "X:\Movies2160\Z\Z\Zero Dark Thirty (2012) [tt1790885]"
Jun 07, 2019 12:54:00.926 [4380] VERBOSE - [FFMPEG] - Rescanning for external libs: 'C\:\\Users\\aj\\AppData\\Local\\Plex\ Media\ Server\\Codecs\\392df4f-2292-windows-x86\\'
Jun 07, 2019 12:54:00.926 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\aac_decoder.dll
Jun 07, 2019 12:54:00.927 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\ac3_decoder.dll
Jun 07, 2019 12:54:00.927 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\dca_decoder.dll
Jun 07, 2019 12:54:00.927 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\h264_decoder.dll
Jun 07, 2019 12:54:00.928 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\hevc_decoder.dll
Jun 07, 2019 12:54:00.928 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\libx264_encoder.dll
Jun 07, 2019 12:54:00.928 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg1video_decoder.dll
Jun 07, 2019 12:54:00.929 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg2video_decoder.dll
Jun 07, 2019 12:54:00.929 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\mpeg4_decoder.dll
Jun 07, 2019 12:54:00.930 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\msmpeg4v1_decoder.dll
Jun 07, 2019 12:54:00.930 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\msmpeg4v3_decoder.dll
Jun 07, 2019 12:54:00.930 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\vc1_decoder.dll
Jun 07, 2019 12:54:00.930 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\vp9_decoder.dll
Jun 07, 2019 12:54:00.931 [4380] VERBOSE - [FFMPEG] - Loading external lib C:\Users\aj\AppData\Local\Plex Media Server\Codecs\392df4f-2292-windows-x86\wmv3_decoder.dll
Jun 07, 2019 12:54:00.931 [4380] DEBUG - Opening 20 database sessions to library (com.plexapp.plugins.library), SQLite 3.26.0, threadsafe=1
Jun 07, 2019 12:54:04.123 [4380] DEBUG - It took 78.125000 ms to retrieve 0 items.
Jun 07, 2019 12:54:04.622 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:09.797 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:14.946 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:54:19.821 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:54:24.614 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:54:29.214 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:33.925 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:54:38.700 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:43.592 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:48.423 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:54:53.289 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:54:58.374 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:03.310 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:08.156 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:13.047 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:17.708 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:55:22.372 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:26.961 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:55:31.572 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:36.295 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:40.991 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:55:45.622 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:50.362 [4380] DEBUG - It took 0.000000 ms to retrieve 123 items.
Jun 07, 2019 12:55:55.015 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:55:59.746 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:56:04.448 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:56:09.090 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:56:13.792 [4380] DEBUG - It took 15.625000 ms to retrieve 123 items.
Jun 07, 2019 12:56:15.103 [4380] DEBUG - Scanning [Cloud] Movies (2160p) using en(Plex Movie Scanner) with 1 current media items and 1 section locations in the database...
Jun 07, 2019 12:56:15.104 [7152] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/notify/cullTimeline?librarySectionID=14&sinceTime=1559903775
Jun 07, 2019 12:56:15.106 [7152] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/notify/cullTimeline?librarySectionID=14&sinceTime=1559903775
Jun 07, 2019 12:56:15.152 [4380] DEBUG - Performing a scan with 'Plex Movie Scanner' (language: en virtual: 0).
Jun 07, 2019 12:56:15.153 [4380] DEBUG - * Scanning X:\Movies2160\Z\Z\Zero Dark Thirty (2012) [tt1790885]
Jun 07, 2019 12:56:15.153 [4380] DEBUG - * Scanning directory X:\Movies2160\Z\Z\Zero Dark Thirty (2012) [tt1790885] (parent: yes)
Jun 07, 2019 12:56:15.154 [4380] VERBOSE - * Noting that 'Z\Zero Dark Thirty (2012) [tt1790885]' was updated at 2019-06-07 12:23:42
Jun 07, 2019 12:56:15.154 [4380] VERBOSE - * Taking directory 'Z/Zero Dark Thirty (2012) [tt1790885]' (81993) out of the map (0 left)
Jun 07, 2019 12:56:15.155 [4380] DEBUG - Adding file for scanner: "X:\Movies2160\Z\Z\Zero Dark Thirty (2012) [tt1790885]\Zero.Dark.Thirty.2012.2160p.BluRay.REMUX.HEVC.DTS-HD.MA.TrueHD.7.1.Atmos-FGT.mkv"
Jun 07, 2019 12:56:15.157 [4380] DEBUG - Skipping over directory 'Z\Zero Dark Thirty (2012) [tt1790885]', as nothing has changed; removing 1 media items from map.
Jun 07, 2019 12:56:15.162 [7152] DEBUG - HTTP requesting GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Z%5CZero%20Dark%20Thirty%20(2012)%20[tt1790885]
Jun 07, 2019 12:56:15.166 [4380] DEBUG - Removing 0 media items that were left.
Jun 07, 2019 12:56:15.166 [4380] DEBUG - Removing 0 directories that were left.
Jun 07, 2019 12:56:15.167 [4380] DEBUG - Refreshing section 14 of type: 1
Jun 07, 2019 12:56:15.169 [4544] DEBUG - Refreshing 0 IDs.
Jun 07, 2019 12:56:15.173 [7152] DEBUG - HTTP 200 response from GET http://127.0.0.1:32400/:/metadata/updateProgressMessage?message=Scanning%20Z%5CZero%20Dark%20Thirty%20(2012)%20[tt1790885]