The motor controller firmware only allows to set speed and direction of motors, there is no notion of tracking state in the firmware. And EQMod can't know that you're pressing a button on the handset before eventually restarting tracking. The same applies to the handset which does not know (or look) whether the mount was tracking before the manual move. A solution would be to start tracking on the handset before the manual move.
When using the synscan driver, it talks to the handset firmware itself, there is an unique state of the mount, I believe.