"What worked for me on an obviously dead Pixhawk:

Make sure your Pixhawk is powered from a stable 5V supply (like the power cable coming from their voltage sensor).
Start MP. Go to the Config/Load Firmware screen and choose.
When it says to "Unplug…"

"I haven't studied the hardware or software enough to be certain, but if I had one that worked as well as yours, I might log the startup sequence and see if there isn't an intermittent  timing issue that occurs only during boot. You could probably…"

"I'm pretty sure that 3DR sent me your Pixhawk, Jacek!

Same symptoms. On just USB, it draws current that's just outside the USB spec. Very different from the last Pixhawk I got. A few percent deviation can be expected, sure, but this is like an LED…"