I was able to reproduce this problem two more times. Same results. My guess is there is an error in the code that evaluates the changes from FTM. When a new alternate fact is created (I've only tested thus far with names), it becomes the preferred fact on Ancestry.com (after syncrhonization) but remains an alternate in FTM.
I have to say. It is a lot of unnecessary work to go back and manually synchronize FTM with Ancestry.com after this happens.