Check if they are terran or atf stations.
Terran rank should be high, and docking should be ok.
But atf rank is looked up. I'm not sure if that is linked to argon rank, which at game start is neutral, or if its linked to the FF rank. No sure on that one.
But its possible that at game start, atf rank is too low to dock at atf stations.
Even for a terran start !
Edit : I didnt see your edits until I went to do an edit
I cant test USC Commander, its not active on my game yet.
Edit 2 : Have you done the save and load asked for yet ? The hotkeys are not set up until the 2nd load.
Edit 3 : 2011 is not a registered text file. I can only assume your game has a script loaded that is using the same commands as something in the mod. Probably Beamdock and Jump to Derelict I'd guess. Check what scripts you have loaded and what resources they use.
Edit 4 : Confirmed, there is a problem with docking.
Edit 5 : Errr....only some of them seem to have a problem. This is bizzare.
What did you do to resolve your docking issue ?
Edit 6 : Issue resolved. Corrupt Dummies.txt in the cat/dat.