A wild guess on my part, but do those files have a ctts atom?
I started the link at that post due to it being the point at which the problem with all those files was found. Your mention of all the problem files being 265 - and I had to re-acquire and repair about 1400 of them ultimately made me think of that.
It wouldn’t take much to make me believe Plex wouldn’t generate a VPT for a file without a ctts atom.
Check a few things, confirm or rule out, then disregard if necessary.
It was worth a shot.
As a test - remux one of the problem files with V45 (or the latest) of MKVToolNix - then see if Plex can generate some VPTs for it.
