Somehow, the driver had gotten messed up and uninstalling and reinstalling it did the trick. I knew I should've realized it when all three axes showed up in the game controllers > calibration page (normally it used to show gas and brake, while clutch was shown in a different box to the side).Has the pedal housing ever been opened? It sounds like the outer wires to the pots were swapped.
Also, which driver software are you using? G-Hub (which seems to cause problems with the old G25 sometimes) or the old Logitech Gaming Software?