Noticed over on TeamRadeon (an ATI fansite judging by the name) they got some ATi response regarding ATI's performance in Doom 3:

"Hi Richard - this is a non issue - Doom 3 isn't even available yet, & we all know that some of our competitors use partial precision where possible. We expect to have updated drivers available in the coming weeks."

More here. So, ummm, basically ATi will (think they'll) have better performing Drivers out shortly & NVIDIA's speed can be attributed (in part) to them using only partial precision.