I recently had the situation where a video showed the same title and thumbnail as those of another (in fact I could see the two side by side), but still played what it actually was on disk and the other one did too.
Refreshing metadata for the library did nothing. Only thing that worked was moving the file to another library–then it showed up correctly there.
Sounds like it incorrectly matched. Fix Match should help there (you may have to split merged entries apart first). Chances are the root of the issue was the file not following Plex’s expected naming/organization (e.g. for movies, using the full movie name and adding the year in parentheses, with any extra information inside of [square brackets]).
These videos this is happening to don’t fit into any of those three categories. They’re in the Other Videos category so you would think they would appear according to the name of their containing folder or their file name as usual.
It’s not that important. Maybe the solution is to just create new libraries. I have a feeling that the whole database of the various libraries needs to be refreshed anyway (I realize that that’ll take a while, though). I’ve also had it happen that the server just doesn’t see certain videos until I move them to another library for whatever reason.
I do have the question as to what the difference is between the “Personal Media” agent and the “Plex Personal Media” one, though.