there are just too many factors present to be able to totally isolate what is causing the benchmark discrepancy. different OSes, different video drivers, and possibly different motherboards. i don't see why an Intel mobo would be using a SiS AGP driver for example. newer BIOSes and drivers don't guarantee better performance, they can actually decrease performance. especially video drivers; wide range of performance there, and i'm sure nvidia is optimizing more for higher resolutions, low resolutions like 640 are plenty fast enough anyway.
but, as has been already stated, it's 640X480. who really cares? the gf4 should still be CPU limited at 800X600 and 1024X768 in many games. i doubt anyone buying either of those systems would use 640.