Ok, we have debug logs to look at. Buffering and transcoding issues is not something I get involved in. But what the heck I’ll take a crack at it, if nobody else will. 
Orderly shutdown of the server shown in server.1.log
May 02, 2017 17:35:05.914 [13120] DEBUG - Ordered to stop server.
May 02, 2017 17:35:05.914 [1152] DEBUG - Stopping server…
Verbose logging being turned off in current server log
May 02, 2017 17:42:01.167 [3268] DEBUG - Completed: [127.0.0.1:49534] 200 PUT /:/prefs?LogVerbose=0 (8 live) GZIP 8ms 268 bytes (pipelined: 12)
File being analyzed for transcoding because direct play is not available.
May 02, 2017 17:44:38.981 [15248] DEBUG - MDE: analyzing media item 3830
May 02, 2017 17:44:38.981 [15248] DEBUG - MDE: Mulan (1998): Direct Play is disabled
May 02, 2017 17:44:38.981 [15248] DEBUG - MDE: Mulan (1998): media must be transcoded in order to use the hls protocol
May 02, 2017 17:44:38.981 [15248] DEBUG - Codecs: testing aac_mf (decoder)
May 02, 2017 17:44:38.986 [15248] DEBUG - MDE: Mulan (1998): selected media 0 / 3830
May 02, 2017 17:44:38.987 [15248] DEBUG - Streaming Resource: Added session 05BB4FF0:16668fecf35b309f0be653713cb99f95
May 02, 2017 17:44:38.987 [15248] DEBUG - Streaming Resource: Reached Decision id=2831 codes=(General=1001,Direct play not available; Conversion OK. Direct Play=3000,App cannot direct play this item. Direct play is disabled. Transcode=1001,Direct play not available; Conversion OK.) media=(id=3830 part=(id=3974 decision=transcode container=mpegts protocol=hls streams=(Video=(id=9325 decision=copy width=1816 height=1080) Audio=(id=9326 decision=copy channels=2 rate=48000))))
Playback attempt - a transcode of an mp4 file located on the D: drive.
May 02, 2017 17:44:39.677 [10312] DEBUG - Job running: EAE_ROOT=‘\?\C:\Users\cyril\AppData\Local\Plex Media Server\Cache\Transcode\Sessions\EasyAudioEncoder’ FFMPEG_EXTERNAL_LIBS=‘\\?\C:\Users\cyril\AppData\Local\Plex\ Media\ Server\Codecs\57aa73f-1206-windows-i386\’ XDG_CACHE_HOME='C:\Users\cyril\AppData\Local\Plex Media Server\Cache' XDG_DATA_HOME='C:\Program Files (x86)\Plex\Plex Media Server\Resources' X_PLEX_TOKEN=‘xxxxxxxxxxxxxxxxxxxx’ C:\Program Files (x86)\Plex\Plex Media Server\PlexTranscoder.exe -codec:#0x01 h264 -noaccurate_seek -i “D:\Movies\Mulan (1998) [1080p]\Mulan.1998.1080p.BRrip.x264.GAZ.YIFY.mp4” -map 0:#0x01 -codec:0 copy -map 0:#0x02 -metadata:s:1 language=eng -codec:1 copy -copypriorss:1 0 -break_non_keyframes 1 -break_non_keyframes 1 -segment_format mpegts -f ssegment -individual_header_trailer 0 -segment_time 1 -segment_start_number 0 -segment_copyts 1 -segment_time_delta 0.0625 -segment_list http://127.0.0.1:32400/video/:/transcode/session/16668fecf35b309f0be653713cb99f95/seglist -segment_list_type csv -segment_list_size 2147483647 -max_delay 5000000 -avoid_negative_ts disabled -map_metadata -1 -map_chapters -1 media-%05d.ts -start_at_zero -copyts -vsync cfr -y -nostats -loglevel quiet -loglevel_plex error -progressurl http://127.0.0.1:32400/video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress
I believe the following is stating that Plex is creating 1 second long chunks to stream.
May 02, 2017 17:44:44.746 [10312] DEBUG - HLS: Building an M3U8 for 5271 total seconds with 1 seconds/segment, target duration of 1.
Transcoding speeds look good throughout
May 02, 2017 17:44:45.153 [15296] DEBUG - Request: [127.0.0.1:50294 (Loopback)] PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=1.7&size=-22&speed=181.8&remaining=28 (43 live) Signed-in Token (sackhouse)
May 02, 2017 17:44:45.156 [8884] DEBUG - Completed: [127.0.0.1:50294] 206 PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=1.7&size=-22&speed=181.8&remaining=28 (43 live) 3ms 326 bytes
May 02, 2017 17:44:45.657 [15248] DEBUG - Request: [127.0.0.1:50373 (Loopback)] PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=3.2&size=-22&speed=151.9&remaining=30 (53 live) Signed-in Token (sackhouse)
May 02, 2017 17:44:45.657 [8884] DEBUG - Completed: [127.0.0.1:50373] 206 PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=3.2&size=-22&speed=151.9&remaining=30 (53 live) 0ms 342 bytes
May 02, 2017 17:48:12.636 [4452] DEBUG - Request: [127.0.0.1:51488 (Loopback)] PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=3.9&size=-22&speed=15.4&remaining=12299 (19 live) Signed-in Token (sackhouse)
May 02, 2017 17:48:12.637 [8884] DEBUG - Completed: [127.0.0.1:51488] 206 PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=3.9&size=-22&speed=15.4&remaining=12299 (19 live) 1ms 342 bytes
May 02, 2017 17:53:20.290 [16256] DEBUG - Request: [127.0.0.1:52546 (Loopback)] PUT /video/:/transcode/session/16668fecf35b309f0be653713cb99f95/progress?progress=0.1&size=-22&speed=19.1&remaining=335 (19 live) Signed-in Token (sackhouse)
Client report buffering 28 times during playback.
May 02, 2017 17:47:02.147 [10312] DEBUG - Client [16668fecf35b309f0be653713cb99f95] reporting timeline state buffering, progress of 104000/5270420ms for guid=com.plexapp.agents.imdb://tt0120762?lang=en, ratingKey=2831 url=, key=/library/metadata/2831, containerKey=, metadataId=2831
1 Why is Plex transcoding a mp4 file to a Roku? Quality settings. Bad encoding?
You should probably provide Plex Media Info xml for that file.
2 Is D: drive a usb drive or a network drive? How is attached to the server?
3 What type of antivirus are you using?