Ah okay. It seems like the itch client unfortunately didn't play nice with the initial post-launch updates. I'm currently looking into how to solve the issue within the app, in the meantime if you can download the updated files manually from the game page if you want a version without this bug. Sorry for the late reply+inconvenience, and thanks for bringing this issue to my attention.
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Sorry for the late reply, and sorry to hear the game doesn't run well on your machine - I know how frustrating that can be.
Itch doesn't have a refund system, but if you contact me at jesse[at]a6productions.com we'll sort it out.
Is it an xinput controller? PS4/3 and non-xinput generic controllers aren't currently supported unfortunately.
If it is an xinput, make sure it's plugged in when you boot the game, and disable any other keybinding software (joy2key, x360ce).
Hope this helps!