You should check with Bob@KMS. He is the AEM guru, and knows how to troubleshoot them better than anyone else that I know of.
I have the AEM v1, and haven't had any issues with A/C with the AEM, so I can't really help except to suggest that you manually trigger the AC system (without the EMS) to make certain that it is working, then check the output of the EMS to verify that it is working. Verify that tje AEM is set to the correct polarity and putputs the correct voltage, and that the amperage draw is within the AEM's limitations.