I have a A-trend 7020V mobo which probably means nothing to you, it uses the Apollo pro 133 chipset with the 693A bridge. Anyway I bought a msi geforce2 mx and stuck it in. To my dismay it did not perform that great. I have a 566 celron 256 ram, windows 98. I get about 60 fps max in quake 3 and a 3d mark scorce of 2300. Anyway I ran some other tests and one said my harddrive was slow but not to worry. Anyway got pissed of and ripped the card out stuck it in my mates computer which is 566 celeron, 128 ram, abit mobo which uses the apollo pro 133A 694 bridge and we got about 86 fps and a 3d mark scorce of 3800. So does a mobo make such a big difference?? And does a hard drive effect gaming performance?? I ask you this.
I any system all componants are important but with such a big difference in fps I can't imagine it's just the mobo. Quake is extremely memory bandwidth intensive, do you have CAS3 100SDRAM while your friend has CAS2 133 or something like that.
I'd also check all driver versions and stuff or reinstall windows fresh and have another go.
Do you have the VIA AGP drivers installed? Are you using the latest Nvidia drivers for the GeForce MX? How do your bios settings compare to your friends, do you have AGP 4x enabled for instance?
Abit boards usually have a more "tweakable" bios and this combined with better drivers could be what is making the difference.