I'm not sure if you know of this, but The Brain in Gecko is horribly bugged, perhaps even more now than without the RP. These bugs occur in every playthrough I've had with the RP v1.2, on different systems and with identical Fallout installations.
1: When I first talk to him, the player acts as if I've already spoken to him. I'm not sure if it*s the original dialogue, in which case it isn't the RP coming short, but I seem to recall there being at least some kind of introduction.
2: When I talk to him with the Hy-Mag in my inventory after having given the optimization disk to McClure but before fixing the plant, he repeats the last line anyone said to me and then crashes the game. This one time I went trading at Percy's before seeing The Brain, and then when I talked to him he said "That'll be all for you then?" and then bombed to desktop.
3: When I talk to him after having repaired the plant and ask him about Festus' optimization disk, his dialogue lines revert to the ones about Gordon's economy disk, which I've already delivered long ago. This happened when I asked him who in VC I should deliver the (optimization) disk to.
4: When I talk to him after having optimized the reactor disk but before optimizing the plant, I get the option to say "We had a deal. Withdraw the creatures and I'll optimize the plant". The problem is, I haven't been to NCR, haven't got the Vault Village's location from Stark, haven't learned of the rat infestation and haven't made a deal with The Brain.
I'm just avoiding The Brain altogether now. Of course, besides him behaving oddly, the RP is pretty much bug free.