I am having the exact same issue and it is driving me nuts. I can’t really listen to music on the go anymore.
I just bought the Hades 2 soundtrack from bandcamp, downloaded the FLAC version, which Plexamp is transcoding to opus (even though I tried to disable that) the second track consistently glitches at the 34 second mark. But only on Plexamp, playing through the web interface, or streaming via Lyrion music player at home have now issues.
I use a synology NAS for storing media, but Plex is running on a Ubuntu server 22.04 VM that accesses the files over NFS.
I am currently running Version 1.43.0.10162 of the server and v4.12.4 of the web app