We ran the multimeter between the + terminal on the PDB and the frame - the pinched wire made the frame positively charged, and we think the plug for the radio then hit the frame, completing the circuit and blowing the 12V output.
As you can see
here, we've gone to great lengths to ensure the cRio is completely isolated - an ESD safe, non conductive plastic mount, and surrounded on all sides with an ESD safe, non conductive foam. The cRio is definitely NOT connected to the frame. Likewise, the camera is mounted on the same ESD safe, non conductive plastic as the cRio, ensuring it is NOT connected to the frame.
Once we fixed the pinched wire, we didn't have any more trouble with our frame, within the limits of the rules/checklist.
However... being as overly paranoid as we are, we did discover a small short with one of the CIM motors. There's no visible shorts in the motor leads (we checked), but we did measure 5-6 M Ohms between the motor lead and the chassis. The other 4 CIM's did not exhibit this behavior. Any ideas on that one?