Welcome to IRV2!
You didn't give any details as to when this happens but I "think" I might understand what's happening.
Check out the following link:
Xantrex AGS Link
Is this the version of AGS you have? THis version interaces with the System Control Panel
which also handles the RS series of inverter/chargers.
This is the AGS system that I have installed in mine. It will kick in the genset in response to a number of parameters, which are all set up by the user ahead of time. It can start when the battery voltage gets too low, it can be set to start when the inverter loads run high for too long of a period of time, and it can be sset to respond to a request for cooling from the air conditioning thermostat.
The problem with this unit is that it does not sense shore power presence. Therefore, whenever the thermostat calls for cooling the genset starts up, even when it's plugged into shore power. To rectify this, I installed a relay that was energized by the shore power side of the transfer switch. Then I routed the thermostat feed leads through the relay contacts so the thermostat won't communicate to the AGS module whenever shore power is present.
Maybe this is what you have?