Hi, I just encountered this one myself and found this thread. Did you manage to find a solution? I wonder if the problem might have anything to with the way the game lets you revert. You know, if you reach orbit, you can then revert back to launch or assembly, or you can leave your rocket/craft there and go to space center. Because I already launched the station core, then went to space center and launched another component, then docked that with it... could that have stuffed it up? Although, I also noticed it when I tried docking with another craft so maybe not.
