I have had FTM for a number of months now, and I've experienced all of the problems described in theis thread. The sync between FTM and Ancestry is unreliable at best. It is a bad application - one at least the sync process is.
I use FTM for reporting process only. And, my online Ancestry as the definitive database for all of my records.
The way I get around it: when I'm ready to report, I DELETE the FTM record. I then redownload the file from Ancestry without the auto1sync option.
It's a long slow process, but the reports I'm producing are quite good (I need reports for a family reunion I'm involved with -Nov this year).
I hope this is of some use to you.