Cannot power Arduino Due with external power (only USB)

Whoa! That's a substantial amount of computing power!

"Real" Dues, or clones? They tend to have different power circuitry. There have been assorted reports leading me to believe that SOME clones might have faulty regulator circuitry or chips (although so far, that's shown up mostly in AVR-based boards.)

Have you traced out (voltmeter or scope) where the power is failing? 12V in, diode, 5V regulator, auto-switch power selector, 3V regulator, ... ?