I have a Microsoft side winder force feedback pro joystick. The game does not want to recognize the keys for it. I can play the game with the mouse but not the joystick. Next to the menu options are number options which show that it detects a mouse but when I go to define keys the game controller shows question marks. If I click on the question mark to try assign a key it does not register when I press a joystick button or move the joystick. It comes up with an 'ERROR READING KEY' after a while.
I have already updated the game with update patch 1.01.
The joystick itself works fine. I can calibrate it in windows control panel, and all the buttons work.
What can I do to play with this joystick?

This is strange, as far as I know the patch solves all joystick related issues. Are you sure the patch was installed correctly?

Please try the solutions from this thread, (although they are pre-patch).

I'll quote the most important bit from the thread:
<<Some types of gamepads or joysticks are not detected properly when combined with some types of USB keyboards (especially Saitek gamepads with Logitech USB keyboards).

If you want to check if this is the problem that affects your game, you can try to switch to a PS2 keyboard or another type of USB keyboard.

The patch fixes this issue.>>

I have the same Microsoft Force Feedback joystick, (and a DELL - probably logitech - keyboard). Unfortunately, after installing the patch, still no success.

The "low sound" problem may have been solved by opening and running the "DXSETUP" file in the Ubisoft SUPPORT/DX folder. Too frustrated to have a look at the moment to check.

Best of luck to the Ubisoft software writers & fixers if they have another go at this problem and try to come up with a patch 1.02. Looks like quite a bit of time and effort has already gone into developing this game.