They added Steam cloud support to the game last month. If "some time ago" was before that, maybe that game update changed how the game sees your controller. If you did anything special to make that controller work with the game, maybe you need to redo it. That's about all that I can suggest.

Ur not crazy. It's always been like that I think simply the game isn't compatible with it on steam at all. It never worked for me even before ur post. I tried DS4 to emulate my controller in hopes it working shi still dont. It breaks my heart cause I wanna relive nostalgia with the controller and idek the computer keys. Im gonna keep trying to fix it if I do ill respond here

I ♥♥♥♥♥♥♥ fixed it.
https://github.com/csutorasa/XOutput/releases
the problem is and I read this from another discussion, it's because this game only works with xbox controllers. Download XOuput from the link I post, configure all the game controlls.
(Add controller, configure each button it will guide you with the xbox controller and just match it on ur ps4 controller)
Then dont panic it still won't work, you then have to go to ur steam settings or press ur ps button while being in game and just attempt to configure ur controller to xbox layout. IF you can't find it or doesn't work, just make sure the xbox controller is checked mark even if it says ur layout is ps4. Sorry my grammar is ♥♥♥♥ but hope this helps you man

I fixed it u need to connect ur controller via bluetooth enable steam input then it will work