I just went and bought a 2nd GTX460 for PhysX (overkill I know) and I modified its BIOS for clocks of 800/2000. Now, I've cleaned out the drivers thoroughly and then updated the BIOS using the following commands from DOS;

nvflash --eraseeeprom
nvflash -4 -5 -6 <filename>.rom

Rebooted, and installed drivers. Now whenever I open any program that tells me GPU and memory speeds they all say the clockspeeds are still stock (700/1800) I was wondering does anybody know if its possible the driver is overriding the BIOS clock settings?