This might sound weird but I tend to play a lot of games with a combination of gamepad in my left hand and mouse in my right. It's just a habit I got into a long time ago and it's useful in a lot of games. Using an analog stick a instead of WASD works much better for me.
Anyway, Starsector is one of those games I play like this. I usually use Xpadder and I've never had a problem in any of the previous versions but for some reason it doesn't work in the new update. Everything works fine when I open Xpadder before I launch but when I'm in game nothing from my gamepad seems to register. Funny though if I alt-tab out, it goes back to working perfectly, mimicking the mouse etc.. but then stops when I tab back in. I've never even seen behavior like this when using Xpadder over the years. Any idea of what it could be or how to fix it?