I'm using the latest version of the 3dnes windows build, and I'm trying to play Battletoads, but I'm controlling both 'toads at once and it's very annoying and difficult that way. Is there are way to disable controller 2 so that this doesn't happen?

Why do you want to play 2 players mode alone?

that's not what ruiner means. when you press P1 start, it also activates player 2. as if both player controllers are bound to one controller. I have this issue with rampage so i know what ruiner means.

Yes, JJXB has it right. I'm using an xbox360 controller and one controller is currently both player 1 and 2 at the same time.

Solution for the time being, plug the second controller then everything will work fine :)

I can do that. Thanks, geod! Keep up the amazing work!

Glad it works for you. I will not change that behavior. Imagine you two guys want to play mario but only have one controller ^-^