Driving Mega2560 from external 5V bricks USB port

Is it possible you blew the 500ma fuse on the usb power input? Since you have a couple bad boards, can you try connecting one the bad boards and check the voltage on the fuse. It appears to be the gold colored smd marked "500J" next to the usb port. See if you have 5v on each side of that. If not, the usb port will not get power. According to the schematic, that is the only way the usb chip gets power.

I used the usb case as ground for the volt check.

If it is blown, it appears you could "jump" that fuse with a second fuse.