Also experiencing this issue. I've found a temporary solution, which is to save your game - if you open the field to rename your save, it'll switch to controller input again. But that's not great, because you can't save at all times.
I’ve found an easier temporary fix than that. All you have to do is press the Windows key and then click back into the game. It seems to be less effective as time goes on. When the issue first appears, the fix works for twenty-ish minutes, eventually only working for maybe a couple of minutes.
Since I originally posted here, I’ve encountered a worse variation of this bug. I booted up the game and it wouldn’t recognize controller inputs at all until I restarted the PC.
