Yeah, that was probably the problem. I always have a couple of pads plugged in. I assume you're using Game Maker based on the folder structure?
If you are, you should probably set your movement controls to variables that = keyboard || gamepad in order to prevent these kind of issues in the future. That's what I've done and it seems to work fine for now.
If that doesn't work with your current setup, then adding a manual controller input options would be much appreciated.