there are many points you can test, but I think I will confuse you if I try to go through all that, open the controller, you must have a hot wire pinched somewhere. I would advise agianst removing the led wires, the more you mess with these the more risk you have burning them out. open the controller test it, remove the chips power supply, test it, remove ground test it. your problem should be found by now
I had one controller, that you had to press and hold the guide button for a few seconds to power it up, the mod lights would come on imidiatly, but the controller would take a second, this was becouse I dammaged the via, during install.
you dont want to touch any of the button pads with your fingers, the oil can damage them. I dont think this is your problem, just putting that out there.