Hey, sorry for the late reply. That does sound weird. The ODE can be powered by any combination, all three power inputs (Molex, USB0 and USB1) have power diodes to ensure that the 5V input into one port doesn't backfeed into the other ports and create any overcurrent situations, so the combination of ODE powered from Molex and plugged into Pi simultaneously should be fine.
Did you both have the same Pis? Some Pis only consume 200mA or so, and some require 600mA just bareboard, and that combined with any USB peripherals like flash sticks could exceed the power output supported by the 2x6 (which was only meant for powering the logic in a physical disk drive, at a few hundred milliamps). A weird Molex-based solution might be to get a 12V to 5V DC to DC convertor and run it off the Molex's 12V pin, as it's much higher current, having been intended to run all the electromechanical parts in the drive like servos and motors.
My only concern with running the Pi/ODE from a wallwart and the 2x6 from somewhere else would be the potential for ground loops, but hopefully that's just paranoia.