Like everyone on this thread I have had Sync problems. I unlinked and then created a new tree but it soon failed to Sync too.
Just tried using the "Compact File" suggestion that is on the Ancestry Help area. http://ancestry.custhelp.com/app/answers/detail/a_id/5146/se...
It claims that it also fixes problems in the files. It seems to have worked and I can Sync again. I will let you know if it fixes it permanently.