I have had these same issues and have stopped syncing my tree with AMT. It seems the sync process often aborts without cleaning up at least the FTM end; maybe AMT also. I started looking closely at the sync report and discovered that a lot of records were being updated that should not have changed. One sync I started after an abort showed 97 records changed even though I had changed nothing. I also have found many dupe AMT people, branches and facts. With a large tree, I don't think we can tell what FMT/AMT is really doing.