Getting back to the problem of what's causing the clicking sounds........ I have an Intellitec converter in my MH and for this type of converter, clicking sounds are usually the sounds you will hear when the isolator relay is turned on and off. It seems this clicking sound is normal with heavy loads on the batteries or when the batteries are low.
Here's how it works: If connected to shore power and the coach battery is being charged and goes above 13.3 volts for 2.5 minutes (no heavy loads), then the isolator relay will close, which will then provide charging current to the chassis battery (or batteries). And when the voltage to the coach batteries falls below 12.8V for more than about a minute, the isolator relay will drop out to prevent the coach loads from discharging the chassis battery (or batteries). Hence the clicking sounds. So if your clicking sounds are about a minute to 2.5 minutes apart, maybe this is your problem.