Plex does not modify your media files in any way, with the exception of being able to delete files if you’ve configured it to do so.
Plex does pay attention to disc numbers, normally. Plex does have one known problem where it doesn’t separate the track listing for a multi-disc album into discs. I’m not sure if that’s what you’re seeing. It looks like this:
If you’re actually editing the track info and seeing ‘disc 1’ where you expect ‘disc 2,’ I’d like to see a screenshot of the mp3tag screen showing the tags for an example album.
Something else occurs to me - is your Plex server fully configured to use embedded tags? There’s more than just the one checkbox.
Another thought: Is it possible that you changed the disc number tags in the files after you added the album(s) to Plex? If so, Plex is notorious for not properly updating changes like this. You may need to do the ‘Plex Dance’ mentioned in that How-To. There’s a link to it for directions.
