If I enter fullscreen, and even if I return to windowed mode, my xbox controller stops working until i relaunch the game in windowed mode.

I'm on windows 10 if that matters

Same thing happened to me.

Same issue. I switched back to window mode, restarted the game, and it worked for a little while. After a bit of play it stopped working again and doesn't start working again after a game restart. Also using [B] to select in the menu's is very counter intuitive to how most games work where [A] is the select button.

Same here with the Xbone controller. 

Hello! I actually fixed this, but forgot to put it into the full game build - I'll upload a new build that fixes this soon.

Yo! I just updated the game - the fix to this should be included within.