One thing you could do is to run the Sync log report to look at the changes in detail that are being proposed. If you do that, be sure to close the FTM program with the Task Manager, NOT Cancel, so that you won't create more issues.
Also, see http://boards.ancestry.com/topics.software.famtreemaker/9684...
I accidentally made a change in FTM when I was looking at a record and then it showed up as a chance in the sync. I have not experienced the specific issue you mentioned though in FTM 2012.