Yeah, happens to me too. It even happens if the Czechs have transit rights through Germany for some reason, even if they have the rights before the decision.
If you save and load the game as the Czech's there's nothing stopping them from moving the corps HQ that's stuck (with transit rights or without, doesn't matter). It seems the AI is keeps alternating its orders though to move or stay and it never gets anywhere.
Good news is after the first vienna award the it sort of resolves itself. Either Slovakia becomes a rump state and the corps moves finally, or... well I'd hate to give anything away.