WOW, don't reformat immediately. I hate when that is peoples first reaction. There is so many things to try before doing that! And many of the following will give you the same results even after reformatting.
Have you checked your display settings? Set them to ATI defaults. (blend of performance and quality).
Also, scores change a little with driver versions.
What motherboard are you using. Maybe it isn't tweaked at all in the bios. For instance, I have an ABIT IS7, P4-2.6, Radeon 9500 pro and i get 13,500 3dmarks in 2001se, but only 3766 in 03 without overclocking. But I have the gaming acceleration (like PAT) enabled and am able to run the F1 settings as well as aggressive memory timings. All those bios tweaks add well over 1000 3dmarks in in 3dmark2001se. Your motherboard may just not have too many tweaks available, and how far you can go will greatly depend on your RAM. But I'd check that. Be careful though IF you don't know what the settings do as you can screw things up pretty bad.
Also, you have 512MB RAM, is it 2 sticks of 256MB in dual channel mode. Or is it 1 stick 512MB or 2 sticks in single channel mode. All these things will account for lowering the score. Add them up and I can imagine your scores could be that almost that low. Especially if the display drivers are set to a higher quality than the ATI blend. Many people are posting scores with the drivers set to max performace, which adds quite a few 3dmarks too.
So please guys suggest other things before telling someone to whipe his HDD clean. Yes often it is neccesary, but it isn't a starting place. He complains about low 3dmarks, not total instability!!!
ABIT IS7, P4 2.6C, 512MB Corsair TwinX PC3200LL, Radeon 9500 Pro, Santa Cruz, Antec 1000AMG, TruePower 430watt