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thanks for the response c: 

I tried your suggestion but the same problem persists. My controller is recognized and working with nyarupad but the moment I launch MM+, nyarupad shows (1) Unknown controller and no longer tracks my inputs. I have no mods enabled on the game that could be interfering, so it is a problem with the base game somehow.

Edit: I fixed the problem!!! 

I added nyarupad as a non steam game through steam and enabled steam controller input for it. In my task manager, I to the properties of nyarupad and set it to run as administrator. 

In the steam controller settings of MM+ I set it to "use default settings" instead of enable steam input. 

I launch nyarupad as administrator, then MM+ and it is working now :3

The controller tracks my input until I open the game, then it stops tracking it and the controller hands are still. The game I am opening is Hatsune Miku: Project DIVA Megamix + and it is installed through steam with a steam controller configuration. If you know how to make this work properly I would appreciate any advice! 

edit: It works while playing other games on an emulator. It works on stardew valley launched through steam. I think the problem is something to do with steam, or maybe that the game is full screen but i dont know. It seems to be an issue exclusive to MM+.