Ran a quick test myself. I ran a fresh start with TESVAL, followed Ralof, Ralof didn't hide when the Imperials came, and the Imperials didn't attack when they opened the gate. Fresh start without TESVAL, and the sequence went the way it's supposed to. /shrug
Wild speculation here, but I wonder if it may have something to do with the SSE optimizations. Normal x87 FPU code uses 80 bits for working on floating-point values, while SSE only uses 32 bits. If some of the rewritten code relies on the extra precision, subtle issues could crop up.
Though I also wouldn't doubt that the engine is a buggy mess, and simply improving the performance of certain bits of code just exposes pre-existing problems.
Bob: "Hey, it looks like we're getting a crash in some odd piece of code, but I can't figure it out. It goes away when I turn off optimizations."
Joe: "Then just leave optimizations off."
Bob: "So when do you want to fix it?"
Joe: "Who said anything about fixing it?"