Trying to get my Sidewinder Precision 2 Joystick working with Freespace 2, but no matter what I do I haven't been able to get the game to actually use the joystick when starting it. I've done the basic things like making sure my joystick works on my Windows 10 machine, and set it to the preferred device. I've tried downloading both Knossos and wxlauncher, and the joystick can be seen in the settings portion. Once I get into the game, the joystick doesn't work.

Have you looked here?: https://www.gog.com/forum/freespace_series#1662762578

Also - when you say "the joystick doesn't work" - do you mean "does not work at all", or just some functions (e.g.: the throttle)?

Because (in case of the latter) someone figured that out here:
https://www.gog.com/forum/freespace_series/will_the_throttle_from_a_microsoft_sidewinder_precision_2_joystick_work_with_thi/post4