I finally got mine to sync today (7/24/12) I had created a GEDCOM file yesterday and was able to link it to ancestry - but not sync it.
I got an email back from Member solutions today and.....Today I was able to open the program, click on file and new, and there was my gedcom file, I was able to save it back to my computer and sync.
I also was able to download my old file that was already on ancestry and sync it back to my computer.
Might try that......if it fails contact customer support and hopefully they will have you upload your file to them so they can look at it.