I've had the same problem and eventually stopped syncing. I had more dupe sources than original sources. The dupes appear to be caused by editing one or more fields with the Source Editor and then syncing with ATM. The same can happen to citations.
I have found a partial fix to the dupe source problem that seems to work: use FTM to merge all existing dupe Sources into a single Source(1) then download another citation for that Source which will create another dupe Source(2). However, Source(2) is structured as FTM/ATM expects so now merge Source(1) into Source(2) and all seems to be normal, again. I have done this with a couple of census sources and future downloads have linked correctly and not caused further dupes. I have also noticed a similar issue with unmodified ATM sources: Many with similar titles have commas and some do not.