Those of us (many!!) who have had on-going problems with the sync probably can't offer you a magic answer. There are so many different issues with the sync that we have learned NOT to make changes in both FTM and Ancestry. Use one or the other as your primary database.
Re-trying sometimes will get it to sync. I've had to completely re-download my tree about every 3rd or 4th sync since I've had it, sometimes more often.
There used to be a good person in the support section, but he got "promoted" he said, so he is no longer available. Support takes about a week to answer, in my experience, and usually offers a link to the debugging suggestions. If they don't work, you will have to re-download or re-upload, depending on where your main tree is if they don't work.
See Answer Link: http://ancestry.custhelp.com/cgi-bin/ancestry.cfg/php/enduse...