This may be an issue with the southbridge. VIA had some problems back then that were mostly worked around by driver and BIOS updates. Try the latest BIOS and see wether different chipset drivers make a difference.

I had no end of problems and performance impacts when using an NEC chipset USB 2.0 card with a VIA MVP3 board.

Switching out to a VIA chipset based USB 2.0 card resolved everything.

Indeed I have solved with an ALI USB 2.0 card but I may still upgrade the BIOS because I still have occasional system hiccups or freezes until I remove/plug back any of the PCI cards.

USB cards require like 3 IRQs which easily leads to IRQ conflict when all devices are in use simultaneously due to PCI IRQ sharing. One way to work around it may be to free IRQs by disabling the built-in USB controller, serial, parallel ports in BIOS. Then Voodoo 2 can get assigned its own IRQ.

It may also be Win9x causing the problems. Sometimes 2K/XP work fine on a configuration that blows up 9x. I shudder at the thought of whether it could be ACPI, PCI PNP, or VXDs causing that. I usually just disable USB 2.0 with it.

My USB was kind of slow and NIC was giving me fits until I installed the VIA PCI Latency Patch.

I have exactly the same problem as user mrfusion92 with USB 2.0 PCI NEC card and Voodoo 2 8MB, except that I have an Intel 440BX chipset.
I would like to note that 3dfx Voodoo 2 does not use IRQs, so this is not a problem. I have disabled all unused ports in Bios (LPT, COM1 COM2) so the IRQ interrupts are free.
I have had this problem since I installed Voodoo2, i.e. for half a year. Previously, there was no such problem with Voodoo1.
So far I haven't found a solution. There appears to be some conflict between the USB 2.0 controller drivers and the Voodoo2 drivers under Win98SE. It doesn't matter what drivers I install for Voodoo2, reference or FastVoodoo or Monster3DII, the effect is always the same.

Older motherboards can be very picky about the USB controller type. Most people have the best luck with NEC based cards. But sometimes VIA et al work better. Depends on the combination of bios/mobo chipset/drivers being used.

I had some free time and tried to solve this problem.
I bought a VIA VT6212L USB2.0 controller, after installing it in the computer and installing the drivers from the VIA website (they are still available even for Wi98), it turned out that there were no longer any problems between Voodoo2 and USB2.0 that existed with the NEC controller. So the NEC controller is the problem definitly.
Unfortunately, the VIA controller did not work very well with my motherboard because the speed was about 3MB/s (tested under Win98 and WinXP) and it slowed down my computer significantly, the CPU load was high.
I returned to the NEC controller, which has a speed of about 25MB/s and CPU load was on the low level.

A partial solution to the problem was to install the Diamond Monster 3D II V4.10.01.0207 drivers to my Voodoo2.
After installing these drivers, you can use the USB2.0 controller without any problems, nothing hangs up. I wrote that this is a partial solution to the problem, because with the pendrive inserted, DirectX/Direct3D does not detect my voodoo2. This is not a problem because I do not use Voodoo2 with a pendrive inserted and I do not use Direc3D under Voodoo2. However, openGL and Glide games work perfectly with a inserted pendrive.

You can still test the ALi USB2.0 controller, but I don't want to play with it anymore. The current solution is sufficient for me.
In another topic, someone wrote that generally USB2.0 controllers in retro PCs are cancer, fortunately the Intel 440BX with my NEC works ok, with a small exception that I described above.

My 2 cents:
Nec is more compatible in older machines like S7 and SS7 than VIA. Nec works in my S7 and SS7 while VIA plays dead (3 different VT6212L cards). It is either NEC or bust.

But NEC is hell. I had secondary IDE lock up during boot with the NEC card. In bios-PNPsection the option "reset configuration data"->enable helped me.

On 440BX, Nec drove me totally crazy. Something always failed, be it Voodoo, NEC, NIC... When I placed a VIA inside, all was well. I blamed the NEC card and ditched it. Today I know, it wasn't a bug but a feature.

So I tend to prefer VIA, if I have the choice. On old PCs I don't have the choice. 🙁