I'm still learning about the specific hardware Brammo used, but it is a standard SAE J1772 connector, correct? It sounds to me like this could be an interlock issue. The two small pins on a J1772 connector are designed to disconnect before the high current lines disconnect, to prevent arcing across the high current connection. One of those pins is the interlock, or "proximity detector", which is used to detect when the charge cable is connected. That connection is also broken when you press the release button on the charge cable. IF that connection is not made, no current will flow.
Normally I would think this would throw a code in the Empulse's onboard diagnostics, but I'm not sure if it does, can anyone weigh in?
Since you used 2 different charge cables, it's likely the issue is not in the cable itself. You said you individually charged each module? How did you do this? Have you disassembled/disconnected anything on the bike?