Both ports should take power, they're bridged together for +5 and GND. If one isn't working, then something up with the connection of one of the ports on the board. You should be able to test voltage coming from the PWR port when the system is running via the OTG port. WIth a meter, you could tell if it was +5 or GND that was 'bad'. But regardless, might warrant a replacement, not sure though.
