SO Do you remember which mod patches? I am running into the same problem. With TLC i found sally stuck in the "airduct" thing. I tried to move her to the next room, but she runs to the forcefield without pressing the button. I cannot press the button for some reason. So, my last hope is installing the same patches, you did. It might be too late, but i reloaded to a save before me entering the engineering core for the first time and that fixed it for me.