I am increasingly having this problem and haven't managed to synch my online tree with my FTM 2012 program for a week ... I do most of my research in the evening once my son (who has autism) has gone to bed (and has stopped using all our bandwidth!)... what was the point of forking out for the 2012 version when I am back to the 'updating both trees' problem that I had with 2011
HaHa ... just read this on the news release for the update:
"Family Tree Maker continues to make TreeSync faster, more reliable"