PS4 controller detected by Steam but does not work in most games

As stated in the title, I can connect my PS4 controller to Bluetooth and Steam is able to recognize it, however most titles can detect it but do not receive any input.
I have one native title that is able to receive input but the controls are mapped incorrectly.
Dolphin and Cemu are able to use the controller with no issues.

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Have you checked this?

Enable “PS4 Controller” in Steam Controller settings - this way games will think you are using XBox controller. If some games know how to use DualShock 4, you can disable Steam Controller support per-game in particular game’s settings.

I have already checked the wiki page; the remapping is helpful but it does not offer any solutions for controls not being registered at all.

I have tried both enabling and disabling ps4 controller layout support in the Steam settings but neither changed anything. I have also tried enabling other layouts but this did not help either.

Maybe per-game issue? Which games have problems?

Specifically I am struggling with Okami HD (which may have problems nativley), The Binding of Issac, Final Fantasy X, and Waves, All of which run through Proton.

I figured out the issue, I had disabled the Steam overlay a while back to save resources. Controller works in all the games I listed except for Waves with the overlay enabled.

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