I’ve just started my venture into Raspberry Pi emulation, and I’m running into some trouble. I bought a USB adapter to use my original SNES controllers, and they work fine when using EmulationStation, but once I load a ROM, I can’t get anything to register. No button presses work at all, but the keyboard does. This is the USB adapter I’m using: http://smile.amazon.com/gp/product/B002IXZ5DE?psc=1&redirect=true&ref_=oh_aui_detailpage_o02_s00. Several people in the reviews talk about how well it works with RetroPie, which is why I chose it. I even tried using a logitech controller, and got the same issue. It worked great in the EmulationStation menu, but not outside of it. One thing I noticed is that some of the guides show a countdown in the EmulationStation GUI when skipping a specific button while programming a controller (see attached image). My version doesn’t have that, even though it was a fresh install from this site today. Is that part of my problem? I know EmulationStation didn’t previously change the RetroPie config, but does now. Here are some specifics:

Pi Model: B+
RetroPie Version Used: 3.6
Built From: SD Image
USB Devices connected: Keyboard, SNES controller adapter
Controller used: original SNES controllers
Guide used: https://github.com/retropie/retropie-setup/wiki/First-Installation

I’ve looked through the wiki and haven’t found a solution to the problem.
Any help would be greatly appreciated!