I am having the same issues that you are having.......I have come to the conclusion that when I close family tree maker Mac2 version completely down is when I have the issue and was having to re-upload my database to ancestry.com each and every time I went into the program.
For the last few days I have just closed the window down with the yellow minimize button on my mac and left my computer up and running.
So far that is the only way I have been able to keep from having to re-upload my data each and every time.
I still say it is an issue with the family tree maker mac2 version software that when the program is closed down completely it loses its syncing ability.
I have had the same issues with tech support - they said no one else was having the issue I was having - and they wanted me to delete the program and reinstall it - I decided to try this other way of not closing the program before I go to the extreme of delete and reloading the program.