A really oddball situation recently arose in Plex. Namely, all of season 3 was picked up in Plex Media Manager except for the 6th episode (“Chuck Versus the Nacho Sampler”). Basically, it jumped from 5-7. I tried a pile of tricks to no avail – moving the folder out and back in, renaming the file to use periods instead of spaces (Chuck.S03E06.Chuck.Versus.the.Nacho.Sampler.mkv), having it as the only episode in the folder (in case for some reason I had a duplicate), etc.
Turns out, the problem is having “sample” in the filename (I suppose there’s a filter for those.. *ahem*… torrents which include samples). To be clear, I’d named the file as so:
Chuck – S03E06 – Chuck Versus the Nacho Sampler.mkv
The fix was dumping “Sampler” from the file name. I changed the name to the following and it worked:
Chuck – S03E06 – Chuck Versus the Nacho.mkv
An ALT-refresh (the files aren’t stored on the local machine, hence the required “alt” to actually rescan the network folder) allowed it to be picked up by Plex.
I’d assume dropping the title completely (and having Chuck – S03E06) would work too, though I like having the episode name in the filename when I’m playing videos on another machine through VLC (Plex clients shouldn’t care – it should show you the properly scraped name including the “Sampler” part). If you’re really irked/OCD about losing part of the episode name in the file name, you could always be creative and try using S4mpler or fudging the name enough that it doesn’t look like it’s a “sample”.