: The window in the center hanger is closed and
: has no switches near it. Aside from the closed window and the half opening
: air shaft door, there are no other ways into the middle contol room that I
: can find.
I just played that particular level of Rubicon to check things out. That door is never in the closed position throughout the playing of that level. It should already be open once you insert the chip. Now, I am talking about the original Infinity version of Rubicon. Were changes made to this level in the AO version of the Rubicon Map? If not, then the only other thing I can think of is that one of the Trooper's guided grenades may have accidently hit the switch in that middle control room and shut the door. There is one Trooper in that room (at least on Total Carnage) and he does shoot at you while you are in the middle bay.