If you try and set your sovereign to autoexplore, it will not work unless you 'unclick' your programmed manual move.
I have also had issues where autoexplore simply stops. can't ascertain the reason as yet, but it might be when autoexplore has to program a move over previously explored areas (greyed out) to unexplored areas (black)?
Autoexplore doesn't seem to target discovered objects? This would be good.
