I too have a syncing problem, none of the data corruption, although I recently ran a data errors report, to discover a whole host "child sort issues". I wish there was a process to fix them all at once rather than visit each family in the report (over 40 pages worth).
I too have gone down the path of compaction, download a new copy from AMT, and produced a new version from a backup file.
I also created a new user account copied the sync log files over, this worked for a couple of weeks then stopped altogether, and i had to re-download a fresh copy.
I did contact support, even sent copied of the error logs, still awaiting an update that.
As it stands now syncing only occurs one way, from AMT to FTM. That is fine as I'm mining the hints for fresh data, especially in the Electoral rolls. Its probably not going to help when I finish the child sorting errors (can't see where they can be fixed in AMT)