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I have my RAR files copied into the watch folder via SCRU (The Scene Release Unpacker). Metabrowser is set to look their for shows then move them into another folder. Files are saved for XBMC.
Folders: COMPLETE --> (copy/unpack) --> UNPACKED --> (moved via metabrowser)> SHOWS
Media location is set to view the UNPACKED folder and the SHOWS folder. Shows will show up as movies at first as they have not peen processed yet. They then slowly move down into the TV area of the Media Collection. I have a couple DVD rips that I know would stay in the UNPACKED folder and not be processed correctly.

(EDIT: After fixing the shows in red under TV I noticed that I can't even manually search for the shows as MB thinks they are movies.)
The issue I'm having is that some episodes for unknown reasons are not being seen as TV shows. Some even only differ by the episode number from episodes that processed correctly.
Some examples:
These are folder names.
New.Girl.S01E12.HDTV.XviD-LOL = file processed, renamed and moved
New.Girl.S01E13.HDTV.XviD-LOL = Not processed
Both .avi files.

Glee.S03E12.HDTV.XviD-LOL = file processed, renamed and moved
Glee.S03E13.HDTV.XviD-LOL = Not processed

Same with Fringe. Everything is the same but the number.

In this example the x264 version worked and the .avi files did not. Show name and episode info look to be good.
Alcatraz.S01E05.720p.HDTV.X264-DIMENSION (.mkv)= file processed, renamed and moved
Alcatraz.S01E01.HDTV.XviD-LOL
Alcatraz.S01E02.HDTV.XviD-LOL
Alcatraz.S01E03.HDTV.XviD-LOL
Alcatraz.S01E04.HDTV.XviD-LOL
Alcatraz.S01E06.HDTV.XviD-LOL (.avi)= Not processed
https://lh5.googleusercontent.com/-HyxoCrYYTuc/Tz1ao0EodSI/AAAAAAAAAhg/_SNUS__wPR0/s912/shot1.jpg

Thanks for any help.