Part of your problem is quite simple....
You have one pedal for player 1 and the second for player 2..... Each player has two pedals. Polepos has the pedals both properly mapped to player 1. (I updated the code myself.)
Second issue which may or may not cause your problem.....
Taken from the polepos driver:
PORT_START /* IN1 - Brake */
PORT_ANALOGX( 0xff, 0x00, IPT_PEDAL2, 100, 16, 0, 0x90, KEYCODE_LALT, IP_JOY_DEFAULT, IP_KEY_DEFAULT, IP_JOY_DEFAULT )
PORT_START /* IN2 - Accel */
PORT_ANALOGX( 0xff, 0x00, IPT_PEDAL, 100, 16, 0, 0x90, KEYCODE_LCONTROL, IP_JOY_DEFAULT, IP_KEY_DEFAULT, IP_JOY_DEFAULT )
See where a hardcoded key is defined? Unfotunately it's very tough to get these keys removed (devs want them in for some stupid reason). What they do is override your mappings. When you define a cfg file or ctrlr file it is *supposed* to override these keys, but due to a glitch in the loading order sometimes ctrlr files don't.
If you want it fixed bug urebelscum, he was supposed to be on it.

Hope that helps,
HAC