This issue has popped up often enough in other threads, I thought it deserved it's own.
Hopefully if someone searches for the issue, they'll find this thread. It's a simple fix.
Basically, the only issue is that pedals must be marked to combined in windows game controller settings.
I think where people are going wrong is either that they aren't setting their pedals as combined, or are setting it up in Logitech profiler to be combined for Crazy_Taxi_PC.exe, but that doesn't apply when you are calibrating the pedals in CTConfig. They must be marked combined when going through the calibration process in CTconfig and CT3config.
Further explanation for the uninitiated:
Navigating to game controllers in windows varies by OS, but for Windows 7, click Start>Devices and Printers.
You should see your wheel listed under devices.
Right click on it and select Game Controller Settings.
Double click on your wheel and it should bring up the wheel properties.
Click on settings and check the box for "report combined pedals"
Click ok to close that window and ok to close the previous one.
Now go through the pedal calibration process in CTConfig, then click "Save and Exit".
Do the same for CT3Config if you have Crazy Taxi 3.
If you aren't using a Logitech wheel or don't want to set up a profile for each game, you'll have to leave them marked as combined.
If you've set up a profile for each game in profiler with the pedals marked combined, you can change them back to separate in Windows.
To have profiler report them as combined, create a profile, then click the edit tab and select "Specific Game Settings".
Check the boxes for "Use Special Steering Wheel Settings" and then "Report Combined Pedals"