I think I found my issue. Apparently it make a difference as to which order you plug in the controllers to the USB hub - under normal conditions, I had the far left slot open, the second slot for my keyboard dongle and then the controllers plugged into the 2 ports on the far right.
When I was testing my new image, I had the bottom opened up and the unit was upside down. I plugged everything in the same as before, except in reverse (since it was upside down). As soon as I rearranged the plugs, all worked as usual.