I wonder if that's the case. I don't have a game controller, however, I did notice in the game logs that my keyboard is added as the first controller:
[2018-02-28 @ 00:29:44.592] [launch/native] out: Controllers: added manager for application, 1 managers active
[2018-02-28 @ 00:29:44.592] [launch/native] out: 1st controller connected: Razer Razer BlackWidow Ultimate 2016
[2018-02-28 @ 00:29:44.592] [launch/native] out: Controllers: Setup controller mapping : ControllerMapping
Could it be that it looks at my keyboard driver and thinks it's a game controller?
I quickly updated the program from itch just now and it seems to have the same issue still. I also noticed that any changes to the control config I make in game don't seem to stick around (tried changing the tech button to T but doesn't keep the change next time I look). I also wonder if that is related.
Let me know if you need any more info.