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Is it just one file (or a few files) or all your files?
I've seen this occasionally with a small number of files that I now believe have an error in them: some players manage to make it through the bad bits without glitching much, others choke and skip ahead past the error.
It seems to be anything I play, but I'm not sure. I originally thought it was a filezilla file transfer issue, but ruled it out because of the player not having the same issue. Your point about some players handling it better brings that back into question.
Annoyingly by it occuring randomly (although at a consistent spot), it's hard to look for. I have media on this machine I transfered via a hard drive dock, and some via filezilla, so I'll have to be closer attention to stuff transfered from the dock.
No way am I ever disabling Direct Stream, though.
Is it perhaps related to the Codec of the videos?
maybe. It happened with a H.264 as well as H.265 though.
This happens in Chrome and other browsers when direct playing remuxes. Are you by chance using a web browser? If so, switch to an installed Plex app.