I have the same issue - changes made in ancestry.com appear in FTM2012, but not the other way 'round.
It has nothing to do with automatic and manual sync.
I resolved my issue by setting up a secondary profile in Windows 7 and syncing from that profile works.
There have been suggestions that the problem might be a registry issue, but no one at Corporate Tech Support has been able to figure it out. It's been on-going for 6 months +. I've learned to live with it by switching to the alternate profile every 48 hours or so, to do the sync.