Hm, the key to a bit higher Framerates might be to tweak your Motherboard if possible.
Since you run a K6-2+, the Bios needs to fully support this CPU. While I guess you already took care of that, double-checking for the K6-2+'s advanced Features (Write Combining, Linear Frame Buffer) with some of the existing Tools might help.
If the Bios does not fully support the CPU, enabling those Features could increase performance somewhat.
Also, if you run a VIA MVP3 based Motherboard, you should try to enable 4way Memory Interleave (increase RAM performance by ~10%)...
Finally, freeing the CPU of all unnecessary background Tasks (realtime Antivirus protection, MS Office background components e.g. Findfast, Firewall, ICQ, IRC, AIM etc...)
That should get you some more performance...
What dazzles me a bit here, is that you (it sounds like it) get significantly get higher Framerates in lower Resolutions (e.g. ~64fps), than in 1024x768 (~40fps).
Especially when already using low Detail settings, there should not be such a big difference, unless you are using a Voodoo3-2000 (143MHz). The Voodoo3-3000 should not bother too much about running in 640x480 or 1024x768 when low details are used.
Only with max. Details I could imagine it going down by 30%, otherwise it seems strange it breaks off at 1024x768 (?)
A final possibility could be to play with some other 3dfxogl.dll (OpenGL ICD) Versions. While many newer ones have more functions, they are often also optimized better for PentiumIII/Athlon CPU's, than for K6-2 class CPU's.
So, using different, depending on current Version maybe even older OpenGL ICD's might result in higher framerates indeed.
The earliest 3dfx OpenGL ICD to fully support Quake 3 should be the V1.00.0508. Anything from there upwards is worth testing, upto V1.00.0761.
Since the 3dfxogl.dll can be quickly renamed/replaced while running under Windows, testing should be fairly easy and quick. This is the last resort I can think of to maximize your System's performance with good chance of success
Hope some of this helps !
Greetings
FalconFly