Looking at the server log it is indicating that your library media paths are set at the movie file level rather than a parent folder like D:\Movies
Also you are using download folders as paths - it is best especially when auto updating is enabled - to specify paths that you do not download into. So at end of downloads then you move the files to the proper library paths
The recommended folder structure is given on this support page
https://support.plex.tv/hc/en-us/articles/200381023-Naming-Movie-files
More support pages for movies here
https://support.plex.tv/hc/en-us/sections/200098856-Naming-your-Movie-media-files
I would recommend you adopt the standards shown first and then we investigate any issues that you may encounter
The xml from this request would show the library paths you have specified
http://localhost:32400/library/sections
Switch to the movies library having paths such as
X:\Movies
Z:\Movies
and TV Shows Library
S:\TV Shows
P:\TV Shows
These are just examples
and below these library paths have your media folder structure as per the guidelines
https://support.plex.tv/hc/en-us/categories/200028098-Media-Preparation
I need to see the scanner log after the a deletion - may be the issue is that there are loads of changes because you are defining the downloads folders as media paths and may be some limits are being reached because you have many paths - i am guessing here
The logs show these scan jobs for the Movies and TV Shows libraries
Mar 30, 2016 17:12:16:907 [6928] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 9
Mar 30, 2016 17:12:34:036 [8040] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 10
Mar 30, 2016 17:42:16:933 [1180] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 9
Mar 30, 2016 17:42:38:976 [1460] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 10
Mar 30, 2016 18:12:16:957 [0584] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 9
Mar 30, 2016 18:12:38:782 [7376] DEBUG - "C:\Program Files (x86)\Plex\Plex Media Server\Plex Media Scanner.exe" --scan --refresh --section 10
When was the deletion and we can concentrate on one - so probably this needs a controlled test - but tidy up your folder structures and paths first
The scanner log should have entry like this
DEBUG - Deleting media item xxx for any deleted media - i cannot see any of that
Also your logs show that you are getting crashes - it is better to investigate and eliminate those before looking into issues as crashing processes may lead to indeterminate results
Mar 30, 2016 13:41:21:972 [1804] DEBUG - Crash Reporter: Uploading crash report C:\Users\Cwluc\AppData\Local\Plex Media Server\Crash Reports\processing_5944\35cb1916-d0ca-46b1-82f7-2ca2d7be4c04.dmp
These crash dmp files get purged on restart and so would need to be captured and copied out of folder
C:\Users\Cwluc\AppData\Local\Plex Media Server\Crash Reports\ before restarting the server- together with the logs. dmp files need to be zipped to upload here