I'm having this problem, too. I was able to initially download my tree, but I kept getting the "An error occured while synchronizing this tree. You can try again later, but if this message recurs, you may need to unlink your trees and upload a new tree from Family Tree Maker" message. It finally downloaded, but only after unchecking the "Update Automatically" box. I changed a lot of people online, it downloaded the changes, but it won't upload the tree to ancestry.
Is anyone else having this problem?