I've had sync issues off and on also, similar to yours.
Try removing any spaces, dashes, slashes or any other special characters from your family tree names. Those supposedly can interfere. Also, look for any odd characters in media names - things like % or & or ^ or # as those supposedly can interfere.
I have done all that, and all the things you mentioned since I've had FTM 2012. And, downloaded my tree from Ancestry more times that I can remember. And, recently had to delete my Family Tree Maker tree again as it got corrupted somehow and was putting duplicates into my Ancestry tree.
The sync feature is a great idea, and great when it works, and still seems to have some unresolved bugs.
Barbara