I'm using the JKGFX Mod to run Jedi Knight, and got some bad mouse issues when starting the game.

Namely, the mouse would instantly "look up" and be unusable when using any Resolution configuration higher than 640x480.

I read somewhere that setting some kind of DPI setting for the executables fixes this, but those don't work for me.
They seem to be Windows 10 only i guess.

So if you are in the same boat, try the following.

Download the latest release of https://github.com/elishacloud/dinputto8 .
Place the included dinput.dll in your Jedi Knight folder.

That fixed the problem for me :)