I thought I remember reading years ago that because of the CPU scaling putting Voodoo 2 cards in more modern computers can cause them to run extremely hot and they hit some wall where the don't scale very well anymore past a certain point.

Have you tried Glide in pure Dos (7.1) on these chipsets? I just tried Vooodoo 2 with Core 2+i865 and X58+Xeon 5660 and i always getting:
Failed grSstQueryHardware error. I tried 3 PCI slots, i still have 2 used by other cards, if could fiddle with them, if there is a chance..

I also tried Vooodoo 3 with X58 and its the same, any game can find the card.. Vooodoo as 3 card is working fine on this board at least for DOS, i have better card for Win9x..

Update: On Conroe i tried all PCI slots except last and i also tried undeclocking to lowest possible 800 MHz still nothing, i tried Voodoo 3 on this board, i get to 1 step further, Blood and Shadow warrior (not supported in V3 matrix i know) are able to detect card, non grSstQueryHardware error, but im getting just blackscreens during game starts, not even 3Dfx logos..

Update2: Finally some success.. Q2DOS - with H3 driver is running on Core 2 E6600 and V3, without underclocking.. 640x480 bilinear filtering - timedemo - 92 FPS, 800x600 trilinear - 62 FPS, 1024-trilinear 42 FPS, 1280-26FPS, 1600-18FPS.

Ok i made QDOS (realmode only, with NOEMS im getting black screen)+TES:RedGuard Demo working too with V3+Core2 Duo at full speed, so my card is able to work with pure Dos and with old Glide games, but there is probably problem with V3 magic variables for games..