I've tested mine with the fastvoodoo driver.
Worked fine for me with 640*480!
But I know that problem, I had it with my Gamewizard V2 in a normal computer.
The driver had a problem with detecting the card, so I had to add higher resolutions in the registry.
I don't remember exactly, but start searching here:
HKLM\SOFTWARE\"3dfx Interactive"\Voodoo2
There must be something with the resolutions as the names and the refresh rates as the values (decimal!) .
If there is only 512*384, you have to add 640*480 and the value has to be the refresh rate.
I hope my expression is not
to ungrammatical!