Be sure to contact Customer Support. Mine worked great for a month, and now won't sync at all. Support has confirmed the problem with my tress and they are testing to find the problem.
Don't know how long it might take. The more people who report problems, the sooner they might get it fixed.
They did need to change my password and unlink my tree.
There is another thread going at http://boards.ancestry.com/topics.software.famtreemaker/7634...
with more reports of sync failures.