I've had issues with the "waiting in queue" thing also.
I just boost closer to the entrance, at which point I hit X and it all works np.
Another issue is flying into a space station with great enthusiasm, hit X, the "slow down to auto-dock" message disappears, and my ship proceeds to slam into the back of the station - after which the docking computer will try to hug the space station repeatedly, because that seems the right thing to do.
Still find these things charming, compared to cheating NPCs!
