Before you go into the bind controls (this game) option in MAME there is another option just below called analog settings, or something like that. Have you played around with the options in there? Like inverting the axes and such? Sorry i'm not being much help, i haven't had this issue and i'm just guessing at things...
EDIT: i did just check my configs, and the accelerator of my G25 (which shows up in windows with the right drivers) is labelled in MAME as Joycode_1_yaxis, so i would guess that part is normal. I would try the analog options above and see if something works in there.
You are using a separate axes for the pedals, not a joint one?