Perhaps if you could take photos of your BIOS settings we could all take a look at them and see if something's off. I have a few of things that might be causing you the lower than expected performance:
a) If V-Sync is engaged, disable it and see if you get the same results
b) Joseph has not mentioned it, but perhaps he ran the benchmarks with the sound off?
c) Which version of GLQuake are you running? Is it the original 0.97 release or one of the later, unofficial ones?
d) Which timedemo are you actually running? Perhaps this could be the case of running different timedemos between the two of you 😜.
e) Are you 100% certain that you are actually replacing "opengl32.dll" in the Quake folder with the one provided by 3Dfx's MiniGL?
f) What's the score you're getting on both timedemos at 640x480?
If I may suggest something, instead of Voodoo benchmarks, try running the patched version of Quake (1.08) which you can also find on Phil's Computer Lab. Then, we can see if your system is being held back with one less variable in there (the Voodoo card). If we notice something off, then we can start pointing fingers more easily and track down the problem.