In my previous run of SongKong, I got into trouble with tracks that have been released multiple times. I ended with tracks that originated on one CD scattered across multiple compilation albums. I am hoping that there is a setting in here somewhere that prefers to pull tracks together when it can.
A related issue is that I have a giant box set of Hayden string quartets, all of which were re-releases. Is there any way to make it prefer the compilation?
Once songs are split across multiple folders it can be difficult to get them back into one folder, but now we have a Inconsistencies section that is really helpful for tracking these things down.
What I would suggest is you run the Status Report task to get a snapshot of the current state of your metadata, then run Create Support Files to upload the report to my server, and then I can take a look and help with the best approach for your particular case.
Each disc should be stored in a subfolder underneath a boxset album folder, then selecting the album folder should cause it to prefer to match all to the boxset (assuming it exists on MusicBrainz)
I uploaded support info. Another case of trouble is that I have two different two-disc sets of the Bach Cello Suites by two different players, and they seem to have converged.