Short Version: Odds are the ISA sound card is the source of timing issues that prevent recognition of your SideWinder 3D Pro in your problematic system, but it could conceivably be any of or the sum total of all your components.
Really Long Version: The driver package was created specifically for me to use the SideWinder 3D Pro with the Creative Sound Blaster Live! cards that I had in all of my Win98 machines at the time. As I was running tests to adjust the timing within the drivers, I discovered that the only way to get the SB Live! cards to work was to fix two (apparently) unrelated timing issues within the driver. The first problem is the specific timing and control sequence to get the joystick to switch into Digital Mode. The second problem is what appears to be a latency (or delay factor) present in the driver that had to be reduced to zero (no latency) in order to get the joystick to function with the SB Live! card. I can only speculate since I don't have access to the original joystick driver source code, but it is likely that for ISA cards (i.e. pre-SB Live! sound cards), the latency is necessary in order for the driver to work due to the slower ISA bus compared to the PCI bus of the SB Live!. If memory serves, the latency is nulled out for ALL of the drivers in the package, and this is why most (but not all) of the folks who are unable to get the modified drivers to work tend to be those users with ISA sound cards.
If you look at the original manual for the SideWinder 3D Pro, Microsoft enumerated a number of sound and gameport devices that they had apparently tested and found to be incompatible with the SideWinder 3D Pro. This is a sign that ANYTHING that causes a substantial deviation from Microsoft's timing "norms" is likely to cause the SideWinder 3D Pro driver to fail to recognize the joystick and put it into Digital Mode. Since Microsoft chose to use software timing loops in the driver, there are a host of factors that impact timing relative to the driver: CPU speed, FSB speed, particular bus settings for ISA or PCI bus (depending on the sound card), etc. This is why I say that any or all of the components in your problematic system may be contributing to the timing failure of the driver. A few people using SB Live! cards have also indicated that they can't get any of the drivers in the package I created to work. This is a sign that there are cumulative timing issues of the system components that wreak havoc with joystick driver on those particular hardware configurations.
As I mentioned above, the two timing issues that I had to address seem to be independent. This means that I could conceivably create some additional driver packages that retain the varying timing for getting the joystick into Digital Mode (Problem One), but also re-introduce the latency that ISA sound cards seem to need (Problem Two). I don't have a suitable system to test if or how the driver would function with ISA sound cards, so other users would have to the testing. I also don't have the time to do this testing right now even if I did have a suitable system. Basically, this would mean users would have to go through one or more additional sets of potential drivers just as you did with the original set and see if they work.
So the question would be: Are you and/or others willing to go through additional driver sets and see if they work? I would need to set up an Open Watcom environment, adjust and recompile the original programs and then generate some additional driver sets. This might take me a little time, but not nearly as much time as the original effort took ten years ago.