Thanks for the efforts guys, after copying the appdata/roaming profiles over, sync works successfully
Before it was creating a new tree in AMT, (not ideal).
Until this gets resolved I guess its a work around.
Under the original profile, sync only works one way, from AMT to FTM, new profile works both ways.
The sync worked up until, 2 weeks or so ago (well that's when it got noticed), been working heavily online.
This might be the time to start a new thread, didn't want to hijack this one.