Ok, first, MLeo is right, docking outside single player isn't normal, a mod enabled that, and it isn't my mod. It is from Defiant if i'm not mistaken.
As GMAN and Jimmy said to have this problem even before GC, I doubt GC causes it... Like I said before, it shouldn't affect docking.
If the starbase is neutral, then that's probably the reason why you can't dock with it (it's been some time since I went there to see it lol). So if it is that, the problem is: Why the starbase is neutral?
This however I also can't awnser cause I didn't found the part of code that creates the starbase 12 and sets it's attributes. Normally, static objects like stations and planets of a system is created in the system script (normally those with a "_S" in the end of the name), however this isn't true for the Starbase12 system. I checked it's scripts, and they do not create the starbase, so another script which I don't know which creates it, and we need to check it to see why the starbase is set as neutral.
But, setting the starbase, or any other ship for that matter, as neutral, can be done from any script, so even if the problem is the fact that it is set as neutral, it may be not in the code that creates the starbase12.