I seriously doubt anyone's ever had this problem, but 11.1 has the new Disc # field and I've spent part of today populating Disc # fields and taking the first number off three-digit Track # fields (i.e. 617=Disc 6, Track 17). And an odd coincidence occurred when I tried to synchronize. I have this 7 disc set that has four different versions of the same song, on Disc 6 tracks 16 and 17 and Disc 7 tracks 16 and 17. MC recognizes that the same name, track number and album won't be able to be differentiated on the iPod and kicks the two Disc 7 tracks out of the transfer queue.
A prompt asks me if I want to continue with the transfer when the sync starts. When I clicked on yes, after the transfer was done uploading the updated files, there were only 300 something songs out of over 2200 songs. This might be a bug with 11.1.49 when the duplicate error comes up. For now, I'm just going to revert all the multi-disc set track numbers to three digits since the songs end up in an order like 1, 1, 1, 2, 2, 2, 3, 3, 3, etc.