In my case, when the sync works, changes from both trees are transfered as expected. The sync process occasionly adds a few duplicate people with no connections, however.
Now, I get a sync error after the sync summary (change log), during "processing changes from Ancestry" and the process gets aborted. None of the sync items appear to be transfered.
Do you see your FTM changes show up in the change log when you attempt a sync? or do you only see the AMT changes?
Do you have other trees synced? You may want to unlink these and work with one file only. All the linked trees status are contained in one XML file. If one tree is having a problem it may affect the sync of the others.
The sync items (sort of a list of changes made) are kept in a .sync file (SQL file). If anything is preventing that file from being written or updated, FTM wont know what needs to be synced. This is unlikily, but make sure your antivirus is not blocking those files and any background file cleanup tasks are not seeing them as temp files and deleting them.
You can try unlinking your tree and linking from a second (windows user) profile. That will tell you if the problem is profile dependent or not.