In the windows game controls control panel, where are the pedals when pressed and not press? (example: brake is all the way down when not pressed and all the way up when pressed.) Are are nothing wired to Zr & Yr axes? Are you sure the pedals are the X and Y axes, and the wheel the Xr axis? You get that weird setup after you try to remap, or does it look that way when you open the UI input menu?
If it's just a remapping issue in mame, you can hand edit the cfg file as a work around. Exit mame, open the cfg file in notepad, and look for the pedals "standard" input "ports". Change them to the correct axis and save. Restart mame and test if it works correctly.