If it makes you feel any better, yeah I had same problem.
I use a DirectPad Pro adapter to connect a PSX DualShock2 to my PC. First game I ever had a problem with it, after 4 years of using this thing. I sent an e-mail to the tech support department, and got a bunch of crap back. Anywho, I bypassed the problem by connecting a cheap USB adapter I had kicking around to connect the PSX pad instead. I figured the problem was specifically related to the DPP drivers, but you have popular commercial products!
So it appears it doesn't like a certain configurations, or driver types rather than it being a glitch with your computer's setup. I'm sure a patch will be released eventually. A half ass support page can be found
here