Also had that Problem. I had another Dockingport (Large) on that craft, when I decupled that the Medium dockingports worked agian. Seems to be related to craft State?
When a Probe core controlled craft has another part, for example a tank of the 1st tage booster as the Assembly anchor it looses connection to Kerbnet (all controll) when that part gets seperated.
Landed a craft on Duna. After launching back into space it kept the "Landed" state and the map wouldnt show orbit lines for it. I changed the state manually in the craft file back to "Orbiting" and that fixed it. The lander also had a problem where when a kerbal got out it fell over.