I have Pentium 4 3GHz on an ECS P4VMM2 Rev8.1 board, 512MB and a 6600GT AGP (obviously) card.
After a fresh Win98SE install the card was detected and Win asked for drivers, as usual.
I first installed the chipset drivers, rebooted and then the Nvidia drivers. After another reboot, the card wasnt detected anymore, showed as a Standard VGA PCI adapter.
I tried to reinstall the drivers but got an error saying something like No nvidia card found.
After a couple of more reboots the card suddenly was detected again, so the drivers were loaded.
Well, that was only once - same problem after the next reboot.

So I figured it might be a compatibility issue, ripped out the board and all and installed an Asrock K7S41GX board, Athlon XP2600+, 512MB, same Win98SE on the same now formatted HDD.
The board worked fine before, with a Radeon 9800XT card.
Instead of the Radeon I installed a FX5900 for better compatibility with Win98 games.
Yeah right…what do you know: same crap going on, card is NOT detected by Windows!
I found this setting in the bios, Primary Graphics PCI or AGP. Makes no difference what you select, I left it on AGP.
The driver can‘t be the problem since I can‘t even install one. Just says no Nvidia card found.
BTW: after the first Win98 start the card was actually detected as a Nvidia card but unfortunately only once.

Only thing I can think of is try an FX5200 card.

Something’s wrong here but I can’t figure out what