Tho I would probably agree with you in other situations, I have yet to find anyway to change the directional controls on the keyboard. Actually, I'm pretty sure its impossible without hacking into the game. In fact in the key config menu, it seems that the game recognizes the axis controls seperate from the buttons. Didn't even have an option to map movement controls, it was just kinda, inherent to the game and controller.
At this point I think it may just be confusing the different axis together. From that, it sounds like a driver issue, but seeing as this is a mostly customized controller that when manufactured was never intented to be used for pc, drivers are limited, and OLD as far as i can tell. I think the last development for it was back in '03 ish.
The current Driver I'm using is PSXpad. I know there's direct pad pro, but i can't figure out how to even get that installed, as it was designed when Windows XP didn't even exist.
So I'm not sure if I just answered my own question or not, but I'm at a loss of what to do now.
If I knew how the game actually internally maps out controls, how the key configure works and why they won't let you change the directional controls, it may shine a light on this, but that would mean that someone, whether its myself or another, needs to hack into the game code. And that's an adventure by itself.