I wanted to get this game to work with the Logitech Extreme 3D Pro joystick that I have recently purchased.

I plugged the stick in, and let windows install the default driver that it located, and I launched the game using the GOG launcher. While playing the game, the joystick does nothing, and when I go into the game options to manually change key bindings, i press the buttons on my joystick and the game does not detect the input.

I went and then downloaded the most recent driver from Logitech and I went through the joystick calibration inside of that tool and it is able to detect it just fine. I launch the game, still nothing.

The logitech driver has the ability to select an EXE to be able to launch programs with specific profiles, so I added the freespace EXE, without the GOG launcher and the Freespace Setup option shows up. It is able to see the joystick there and the windows calibration tool is working normally, so I launch the game, same issues, not able to use the joystick inside of the game.

Anybody have any idea what is going on?
I am running Windows 7 Professional

Nevermind, I got it working and now I feel really dumb.

I tried to launch the game through the normal Freespace launcher, not the GOG launcher and the game was defaulting to no joystick. I forced it to default to the Logitech joystick and I unplugged all other controllers (like my xbox 360 controller) and now it seems to be working. The thing is pulling to the left a little bit, but with some calibration i think that will go away.
Every time I try to launch the game with the 360 controller plugged in it will try to default to the 360 controller. So I would have to re-launch the calibration tool and select the logitech stick again.

I have the same stick - I think some older games only take the "first" peripheral to be the one you want so that if you have more than one they get confused.

BTW - have you thought about downloading the Freespace Open Engine? It is really nice - makes the game feel very modern with beautiful graphics and a lot of fixes/updates which help with compatibility to modern OSes (including OS X and Linux).