UPDATE: After some great suggestions here, I got everything working. Was a Linux permissions issue mostly, but also some files were not named properly. Everything is working as I'd expect, all be it, a bit slower than PLEX used to, but I'm fine with that.
I have a Library called Star Trek Movies, in this library is my collection of 1080P 10-bit MKV files of said collection, correctly named, and did work perfectly fine in PLEX. However, only one file will be pulled into the library and it won't ID that file properly. Does anyone have any suggestions of what could be the issue? I'm having the same issue with other folders of movies as well. Haven't tried to add any TV Shows as of yet though.
Edit: I do get this error a lot in the log, but I can't seam to figure out what it means.
"External request received, however, only an internal interface bind found."
Permissions seamed to be the issue. Everything is working, all be it, a bit slower then plex used to. But least it's working.