I've included all three ports available at the current stage in my career game. I play a heavily moderated game, so I have no doubt theres a conflict happening. However I have removed all the docking mods I could find on ckan, and it still persists. Testing has shown that it might be an animation glitch, since the status changes when I extend the "bumper", an addition to docking ports done by Ven's Stock Parts Revamp. I'm going to uninstall that mod and the one that adds the third docking port you see on screen momentarily and will return with news of how that affects things.