Have you verified that Plex is completely configured to prefer local metadata? Since it was working in the past, I’m sure you’ve done this, but it never hurts to double-check.
Disc numbers are very important on multi-disc sets. In my experience, if they aren’t there, Plex can be very unpredictable in how it catalogs the set. I’ve seen Plex create Disc 1 with 1 track, Disc 2 with 12 tracks, and Disc 3 with 30, and there were only two discs in the set. And this was 2 or 3 years ago, before the recent changes. Adding the disc numbers to the metadata fixed it immediately.
Something else I noticed: In Musicbrainz, the 3-disc version of this set is entitled “Man on the Rocks (super deluxe edition),” and the “Man on the Rocks (deluxe edition)” is a 2-disc set. I don’t know if this is important, but you might try making the title in your tags match what MB has exactly. I know Plex is picky about the artist name. Maybe it is about this too.
The recent changes to Plex have made some great improvements, like eliminating the Plex Dance. But it also seems to be much more sensitive and unpredictable if tags aren’t precise. Whether that was necessary to fix other issues, I don’t know, but it appears to be the case.
