Is it tripping the breaker for the second A/C when it makes the "different" noise? If not then my money would be a bad relay. Here is another test, turn off all the load breakers that are hooked to the EMS then start the process. With all breakers off it should go through its cycle and stabilize. If it does then start turning on breakers except for the one that make a funny noise when the relay trips. Or maybe that is what you alredy did and if so I would go back to my money being a bad relay. I will say though that if you call Intellitec they have great customer service.
Command Master Chief (USCG, RET)
Full Timing in a 2007 American Coach Eagle 45H towing a 2015 Ford F150 4x4 hauling a 2015 Anniversary Edition Honda Goldwing