I am in a similar situation to you atm MadMatt, and I have taken my card back, its a 7800 GS, the store ( Gamedude ) has it and as they say are 'testing' it... they rekon in a couple of days they will "have another card ready" - so i guess mine is being replaced.
all this to cut it short, your card is still in warranty, so my suggestion to you is to take the card back ASAP, I would tell them that it is NOT 3dmark03 now it 3dmark06, and it is not performing as it should be in most games. Get it switched for a new one mate.
I am assuming that if your card has a power jack on it that you have connected it to your PSU..
also, that you have removed your previous drivers, and installed the newer required ones.
Lots of people talk of a temperature monitoring tool for Ati cards to download called ATItool
get it here -