I'm having the exact same problem. It only happens about 2/3s of the time but since I'm building 2 craft in orbit at the moment it's very annoying. It doesn't seem to matter whether I'm using mechjeb or manually rendezvousing at about 2-300m from the station I can't control the movement of my craft at all until it gets 500m away. Things like lights, solar panels, etc still work - just no movement or throttle.