@CrossRoads: That is apparently not the only problem with powering the Mega with the 5v bus. If the USB is powering the Mega, and the 5v bus is being powered directly, The USB power bus and the 5v bus are connected with a FET, and that causes the USB IC to fail.
Take a look at this schematic. The thread link I posted above that deals with this has this solution if you want to prevent damage. You must remove the FET T1 (bottom of the schematic). If Vin is not greater than 6.6v, the USB and 5v power buses are connected, and that appears to cause the USB fail.