When Due is powered with 12V or 9V wall-warts (both are more than 1A), USB Host voltage drops from 5V to 0 in about 2 seconds after powering on, which I saw after sticking a multimeter in there. I 'm using the USBHost library with a corded USB mouse. Everything else on the Due seems to be operating normally since it continues to display stuff on a monitor via VGA.
The mouse is working when Due is powered via the USB Programming port.
Also, the Due is a clone.