I think the OP did indeed do a sync. Although I don't have my copy yet, from what I've been reading you need to start with one tree as the master, and create an 'exact copy' of that tree in the other place and then sync from then on.
You can start with an AMT and download to FTM, or start with FTM and upload to an AMT.
This seems perfectly logical.
1) if one didn't do this, there could be massive differences between the AMT and FTM tree that would be difficult to resolve.
2) I suspect that the initial sync (in either direction) creates some kind of unique identifiers for people that are common on both trees, and that is used from then on to compare records for changes.