I'm trying to play Freespace 2 on my laptop but the game doesn't seem to recognize my Thrustmaster USB joystick. I am on Windows 8.1. The mouse control works, it is just the joystick that is not recognized. I went into my Control Panel to check the device and it is there and is the default for games.

The joystick works fine for Star Wars X-Wing.

Any insights?

See if you need to select it in the launcher, I don't remember because the last time I played this was with the FSO mod.
Also, I think the game defaults to the first controller in the windowspanel, so if your Thrustmaster isn't the first you may need to change the priority or rebind the controls in the game.