There is a check made when doing a sync to see if there is duplicate information. If it finds duplicate information, it gives the following message:
"You are attempting to transfer multiple tracks with duplicate information. Would you like to remove the duplicates and continue with the transfer?"
I think this check is based on matching the tag information - although I'm not 100% sure about that. Assuming I'm correct, I do not think Disc # is being considered, and I believe it should.
As an example: I have an album called Thirty Days. It is a 17 disc set by the Beatles. It's the making of Let It Be with lots of duplicate track information - outtakes, rehearsals, etc. Everything was fine with the way I had this setup. I had the disc # in the album name. I did not use the disc # tag. I changed this over to remove the disc # from the album name and use the Disc # tag. It now shows duplicate information and I cannot sync that album. As a workaround, I changed the it back to use Disc # in the album name. Everything works fine if I do that.