When this option is off (the default), even “pregap” hidden tracks are numbered from one, not zero, so other track numbers may appear to be bumped up by one. When it is on, the pregap track for each disc can be numbered zero.
I have per_disc_numbering on, so maybe this is only a problem with musicbrainz?
Hmm; it looks like it’s numbered right in MB. I’m not entirely sure what to suggest—if you’re feeling up for it, maybe consider diving into the beets.autotag.apply_metadata function and printing out a few values to see if you can see what’s going wrong for that track?
Or, it might just be a problem in the printouts from the importer. You could try applying the match and then seeing if it does the right thing (even though it doesn’t say that it will).
Thanks for the idea, I tried to import to see what would happen and it seemed screwed up so I did some more digging and it looks like CueTools screwed up the tags when it made the files that I was trying to import
I fixed the tags and then reimported them and it showed this: