The issue I think is with the Arrow recognizing a docked vessel. I just ran a flight of an XR-2 to an Arrow in 1000km orbit. I docked at first to port 2, on the top side. All is well, eva crew to the arrow, alright.
Then I open the bay doors and move the XR-2 from port 2 to the bay. When I dock to the bay, I get the sound to play, the XR2 says it is docked, the Docking MFD says it is docked, the Pursuit MFD says I am docked, but the lights in the docking bay remain in that blue sequential pattern as if to say, this port is still open. I switch over to the Arrow and in the VC, I look at the main status screen, and it shows Bay port OPEN. I close the sim, reload the current situation and now the Arrow sees the XR2 and the bay lighting pattern is in that red pattern to say this port is OCCUPADO!