I've thoroughly investigated this problem in the past and I can say at least two things with a fair degree of certainty:
- the issue is without a doubt related to the BIOS, but it's NOT related to normal BIOS settings that one can find in the CMOS setup (whatever it is, it's something more low level). It might be related to other hidden chipset registers, but I have my doubts - it seems to go deeper than that.
- the problem was introduced sometime in early to mid 2005 (I have yet to see a motherboard with a BIOS from 2004 that has this problem), and it's not specific to only one vendor, so I suspect that it's a code block that originates from VIA itself)
Unfortunately, some newer motherboards (such as the Asus K8V-X SE) exhibit this problem with all official BIOS versions (since even the earliest BIOS revision is from mid 2005).
My "solution" in this case was to simply try BIOS versions from earlier (similar) motherboards that do have 2004 BIOS revisions (the Asus K8V-X, in this case) and this actually worked surprisingly well.
Now, here comes the kicker: I have (what appeared to be) two identical K8V-X SE motherboards - same revision and all. However, only one of them worked with the old K8V-X BIOS versions, the other failed to POST after the BIOS update (froze at a memory related post code). So I took off the north bridge heatsinks, and lo and behold, even though both motherboards look identical, their north bridges certainly are not (the North bridge with the round, grey metalic area appears to be a newer revision).
Funnily enough, the one that failed to work with the vanilla K8V-X BIOS, did work just fine with the... (drum roll)... Asus A8V BIOS (which is actually a very different socket 939 motherboard that has the VIA K8T800 PRO chipset). The only issues I could see was a warning message during POST that the "BIOS is not valid for this motherboard", and incorrect/broken readings from the temperature/voltage sensors in the BIOS itself (in Windows they are read correctly by software such as AIDA64). Other than that, the board worked perfectly during many days of testing (and, of course, the Win98 performance issues were gone).
WARNING: don't try this at home, unless you understand the risks (including the fact that you will most likely need an external BIOS flasher, since things will certainly go wrong during the trial and error phase).
2 x PGA132 / 5 x Socket 3 / 9 x Socket 7 / 12 x SS7 / 1 x Socket 8 / 14 x Slot 1 / 5 x Slot A
5 x Socket 370 / 8 x Socket A / 2 x Socket 478 / 2 x Socket 754 / 3 x Socket 939 / 7 x LGA775 / 1 x LGA1155
Current PC: Ryzen 7 5800X3D
Backup PC: Core i7 7700k