I had the exact same problem
First time I played I watched all the intro films and performance was good
All the rest of the time the performance was really bad, even on the menu screen it was really slow.
I don't want to watch the intro movies again and again so I was always skipping them, it crossed my mind that it could be the Obsidian movie but that didn't seem very likely so I didn't bother until I read this
100% fixed all performance issues, title screen is nice, so is ingame
I thought it might be my FX5600U as it's a bit lacking when it comes to PS
I now run with AA and AF, even with both these on it runs better than it does if I skip the Obsidian movie and have AA and AF turned off
It seems to have something to do with whatever they use to show the movies, they always stutter a couple of times and if I skip the ship travelling to a different planet movies I lose all sound effects until I leave the ship and it loads a new area
(I used to get similar performance problems with Hitman3, esp the title screen, maybe it was the same thing)
AMD 2500+
512MB
GeForce FX 5600 Ultra 67.65
SBLive 5.1
