Games fail to recognize some USBHID devices

I noticed an issue where some USB joysticks and button boxes weren't being recognized on proton versions newer than 4.11.
These joysticks are recognized by the native OS, both through evdev and js*, however, any version above 4.11 fails to recognize it.
Thinking it was an SDL issue, I tried sdltester, which includes a joystick tester for both sdl and sdl2. sdl2 sees both joysticks, however sdl does not. This behavior is also seen in most games.

Relevant proton.logs from several versions, as well as system information once I've had a moment to rest.

Original message where I noticed this:

Having issues getting a winwing button box to recognize in DCS. I've got it working natively, IE evdev sees it, but DCS doesnt see it, even if its the only thing plugged in. Any ideas?

Edit: Interestingly, it works on 4.11. This isn't an ideal solution, as this makes VR a lot harder, but it's a clue to as what might be going on.

Originally posted by @SirRolls in https://github.com/ValveSoftware/Proton/issues/1722#issuecomment-933064014

Start by reproducing the failure with the affected USB joysticks or button boxes, comparing Proton versions newer than 4.11 with 4.11 and running the SDL tester. Then compare the provided Proton logs and system information, focusing on the difference between SDL and SDL2 detection. Done means the affected devices are recognized by games on current Proton versions.