your controller may be trying to drive the LED's on a floating ground... since the controller effectively switches the negative of your LED's to it's ground to "turn them on" ... you need to make sure your controller and your LED's power supply are sharing the same negative rail. you may have to tie one of the negative power leads from the power supply to the controller/computer ground or shield so they are switched to the same ground potential difference. (and not just the negative ground potential of the computer the controller is attached to.)