Maybe 🤔 it is not configured well, and some additional instructions are not used, or it could be the BIOS that does not recognize the presence, the problem can be easily solved, using specific programs, I would recommend Phil's benches, in his YouTube channel he talks about a recently updated DOS program, which you can find here:
https://m.youtube.com/watch?v=Po_oy7VjLu0

@geertjanb
Which motherboard?

For best hardware performance I would use
256mb SDRAM PC-133 ( 2x128mb )
IDE Compact Flash card as a Hard drive
SP3 core updates option
DirectX 9

In Bios you could Disable all ports not in use
Increase your Virtual memory settings in Win98

I like this one. Come with a bracket to mount in rear of case or in front bay.

Intel486dx33 wrote on 2025-01-13, 09:27:

DirectX 9

Why install that when the "best" GPU in the machine only supports DirectX 6? Voodoo 1 is only DrectX 3 I think.

Do you exceed the maximum cacheable area of your motherboard with that amount of RAM?

Unless you are running some unofficial patch or engine update, Duke Nukem 3D doesn’t support glide or any other 3D api. Are you launch Duke3d thru Dos or with Win98 overhead? That almost rules out the Voodoo1 being an issue.

I’d do some general benchmarking as see if you can narrow it to CPU/Videocard/disk performance.

Things to keep in mind:

- If you are on an Intel chipset, chances are your motherboard cannot cache more than 64MB. Check your motherboard and the chipset used.

- Yes, USB devices can be problematic. Get yourself a PS2 keyboard and mouse, disable USB controller in BIOS and try again.

- Do you use a HDD or some form of flash media? Do you have DMA enabled?

In general, you should try a few benchmarks to compare with other systems on here. But by all means, K6-2 400 performs roughly like a Pentium II 233-266 in most 3D games and the Voodoo 1 is also pretty slow. Don't expect more than 40fps in Quake 1 512x386 (less than 30 at 640x480!).
Duke 3D has some weird issues with sound stuttering, I wouldn't pay it any heed.

If you're running Duke3D under DOS, you'll probably want to run smartdrv beforehand (the specs leads to assumption of FAT32 here)

Intel486dx33 wrote on 2025-01-13, 09:27:

For best hardware performance I would use 256mb SDRAM PC-133 ( 2x128mb ) SP3 core updates option DirectX 9 […]
Show full quote

For best hardware performance I would use
256mb SDRAM PC-133 ( 2x128mb )
SP3 core updates option
DirectX 9

Sorry but these points are all wrong.
Unless OP has one of the elusive MVP3 boards with 2MB of external cache or late stepping Aladdin V, then 256MB will be outside of the cacheable area and perform worse than 64 or 128 MB.
All the unofficial Windows 98 patches made things worse every time I installed them. So I definitely recommend to stay at vanilla 98SE install.
Voodoo1 and Voodoo2 doesn't like newer directX versions and it can cause trouble very often. For the best compatibility it is best to keep the default directX 6.1 or DX7 if you really need it to run some game... which is very unlikely in this case.

Also the latest Voodoo driver V3.01.00 didn't like K6-2 last time I tried. I suggest to use V3.00.01 instead. It lacks OpenGL ICD, but for Voodoo Graphics that is not very important anyway.

havli wrote on 2025-01-13, 16:58:

Sorry but these points are all wrong. Unless OP has one of the elusive MVP3 boards with 2MB of external cache or late stepping […]
Show full quote

Intel486dx33 wrote on 2025-01-13, 09:27:

For best hardware performance I would use 256mb SDRAM PC-133 ( 2x128mb ) SP3 core updates option DirectX 9 […]
Show full quote

For best hardware performance I would use
256mb SDRAM PC-133 ( 2x128mb )
SP3 core updates option
DirectX 9

Sorry but these points are all wrong.
Unless OP has one of the elusive MVP3 boards with 2MB of external cache or late stepping Aladdin V, then 256MB will be outside of the cacheable area and perform worse than 64 or 128 MB.
All the unofficial Windows 98 patches made things worse every time I installed them. So I definitely recommend to stay at vanilla 98SE install.
Voodoo1 and Voodoo2 doesn't like newer directX versions and it can cause trouble very often. For the best compatibility it is best to keep the default directX 6.1 or DX7 if you really need it to run some game... which is very unlikely in this case.

Also the latest Voodoo driver V3.01.00 didn't like K6-2 last time I tried. I suggest to use V3.00.01 instead. It lacks OpenGL ICD, but for Voodoo Graphics that is not very important anyway.

Beat me to it, I concur 100%

Thanks for your responses. To answer the questions:

It's a Lucky Star 5mvp3 rev 2.1 motherboard (theretroweb link)

For storage i use an IDE to compact flash adapter which reaches around 60 MB/s read speeds under windows 11.

In general the PC is very stable, everything just works. 3DFX, LAN, USB, MIDI.
It just feels like something is bottlenecking and causing stutters.

I will run the benchmark suit!

Also there is a lot to setup in the bios about ram timings (which are now set to normal), AGP Aperture size, AGP writeback, etc.

Booted in (w98) dos mode:

Quake 1:
Software mode
320x200 = 969 frames 15.5 seconds 62.6 FPS
640x480 = 969 frames 50.4 seconds 19.2 FPS

Windows 98 SE:

3DMark01
800x600 @ voodoo1 = crash
640x480 @ voodoo1 = glitches = hang on test 14
800x600 @ Matrox G100 = 353 | 3D Marks - 4613 | CPU 3D Marks

In general i've noticed:

voodoo driver 3.00.01 = works
any other driver like 3.01.00 = crashes as soon as any 3Dfx game starts but monitor settings does show 3dfx logo.

Could this be the issue?

After enabling DMA