Re: PC thinks I have two controllers but only one is plugged in.

I do not know a solution, I'm just a player like you, but would like to share my thoughts.

did you already check whether there are still two (or more) controllers listed as active in the Windows settings? I assume that Madden uses the information directly from the operating system. I had a similar issue with disconnects last year because two network ports were listed as active, although I had unplugged one of them. I'm not used to controllers on PC so I cannot give you more details. but this would be my first guess. maybe it's worth to google for how you can activate (and deactivate) controllers.

hope that helps.