I don't think it's Windows' problem, I think it's the problem of the USB adapter, or more specifically, its drivers.

I've tried a couple of those adapters (in my case, Gamecube->USB adapters), and I've found that their drivers are very iffy, on the verge of being unusable. As it stands, I was only able to get the analog finger triggers to work as throttle and brake by electronically modding the joystick itself.

I'd google for people on forums with your same problem and see what their workarounds have been.

It's possible you might be able to edit the INF file for the driver to remove the phantom axis.