I do not believe this is related to PCB layout because as explained, this happens on multiple different chipsets and multiple kinds of boards. If you are referring to PCB of the video card, I have tested this on 7 different Voodoo1's (some with standard 4MB, 3 being the Canopus Pure 3D with 6 MB), and 5 different Voodoo 2 boards used as Voodoo1's, by priming them during boot using the initialization variables.
https://www.vogonswiki.com/index.php/3dfx under Getting the best compatibility
Voodoo 2 DOS Glide compatibility matrix Linked to from that article
Specifically the games that I'm talking about that demonstrate this are Whiplash/Fatal Racing, EF 2000 w/Tatcom+ patch, Starfighter 3000, Battle Arena Toshinden and Descent 2 official 3dfx patch. DOS Glide Games List
This started first becoming evident for me back in the day when the first Athlons Cartridge CPU's came along, and the Athlon A 462 socket processors that followed as their purported FSB is 200 Mhz , Actual bus frequency is stated to be 100 MHz, but because the processor uses Double Data Rate bus the effective bus speed is 200 MHz - but is also evident on Intel boards as when I started getting 2nd and 3rd (or 1oth) computers laying around that are socket 370 Intel 815E or the Via 694x, I found that if a CPU that normally operated at 133 Mhz FSB was limited to 100Mhz, these old games run fine. When the FSB is increased slightly, the games still run but with graphical artifacts like black boxes transposed across the view, and when at 133 or higher, the result is a black screen. Trying to play these games on any hardware newer than a Pentium 3 operated at 100 Mhz FSB, or the later celerons (like the Tualitan Celeron which natively operated at 100 mhz fsb), results in a black screen. I honestly first remember I started noticing this with a Slot1 550 MHz Pentium 3 EB that I was easily able to overclock to 733 by increasing the FSB up to 133- sure I could get my CPU to run faster and is ideal for 90% or better of the games I wanted to play back then, but when I wanted to play these games, I had to clock it back for compatibility.
Here is an old post I know I read before that basically agrees with everything I'm going on about.
Monster3D 3Dfx Voodoo1 on 1ghz system hangs
