I can't seem to figure out what is wrong. Every time I click an area to map a key it changes it to my mouse's left click and won't let me set up my controller. I have tried all of the compatibility options and searched and searched but it looks like my problem is either unique or people are keeping it to themselves. Has anyone had any luck with this issue?

I too have this problem, please let me know if you find a fix!

Chaps....

Go to this thread - solution appears to work for most people.

http://www.gog.com/forum/star_wars_rogue_squadron_3d/controller_support

Protagonist187: Posted the following...

HOW TO FIX THIS ISSUE![

Right click on the shortcut and disable compatibility functions. It's messing with the GOG installed settings or something.
Start the game.

If you're having issues with defining the joysticks buttons (just giving you 1 button) just click on the default button whilst on the joystick option panel, it's on the options on the right hand side. It will define all the controls for you and will work in game.

Now all the menus will work fine, no slow down, and the 360 controller should work fine.

Go to the GOG folder, right click the exe for the game, not the shortcuts, disable compatibility and it works, I have it running on the HTPC with the wireless 360 controller and in my pc with a force feedback joystick Look for the exe, not the shortcuts and disable compatibility, it recognizes the controller right away, you will be able to tell because you can skip the intros with the buttons.

Thanks, y'all. It works beautifully. I'm surprised I didn't think to try this.

On a related issue I can't figure out which buttons control the brakes. This would really help against those AT ATs!

Z Axis by default on the 360 controller (L trigger; and the R trigger is afterburner / overdrive / whatever)