5 minutes later and I have solved my problem. It was a vista setting under Advanced boot options in msconfig. It seems a setting had been set to only use 4 cores. With HT enabled this was trimming out 2 logical and 2 physical cores. With the setting disabled it's booting with 4/4.


EDIT: Well, it turns at Folding@Home isn't hyperthread aware, so all of this who-har was next to pointless  such is life

You don't need a floppy to flash it, there are other options. The first, flashing from windows, is risky but you won't lose your settings as long as you untick the clear cmos option before flashing. You can get the ASUSUpdate utility from the Asus website. To use it you can either get it to download the ROM itself, or you can download it and point ASUSUpdate towards the file. I find that its downloads are unstable, so I download them myself. This works for upgrades but it CAN'T downgrade a BIOS. This is the most dangerous because if Windows crashes during flashing, you've now got a very expensive brick in your case.

The other option is to put your ROM onto a flash drive, reboot your computer and enter the BIOS. Go the Tools tab and select ASUS EZ Flash 2. It will launch into a DOS based flasher. When you're in it select the ROM file and it will flash the BIOS. Unless I missed an option, this will clear the CMOS and your settings but will alow you to downgrade.

Look in the manuals you got with the P6T and it will give you more detailed instructions. The ASUSUpdate can also be found on the disk that came with your board.