I recently started running any% nmg 1.2.2.1 and I have this consistent issue where sometimes the game will stop reading inputs from my controller. I've confirmed I don't have this issue in any other game on steam with the exact same set up. It usually begins happening later in the run, typically by the time I hit Fog Canyon but occasionally I'll have it in the first aspid room. If anyone knows what's going on or has a solution I'd greatly appreciate it.

I have a kind of semi-similar problem with mouse inputs (yes, I use mouse to attack) not registering when loading into the game. I have to open keybinds and then go back to the run. This potentially cost me around a minute in the overall any% run.

Regarding the mouse inputs, you can go to the Third Party Programs portion of the game rules, and there is a program there called blue.exe. It was created to specifically fix this issue.