I experienced this problem on my new 2005 Alpine 40FDTS - after about three days parked the chasis batteries were dead! The drain from the Xantrex brain runs them down that fast. This happened even when hooked up to shore power or when regularly running the generator - i.e. the Xantrex inverter was not charging the chasis batteries at all.
By the way, when the chasis batteries run down, the Xantrex shuts down, the battery boost switch won't function and you can't start up the Onan generator. Not a good situation if you are boondocking. Western RV suggested turning off the chassis battery isolate switch every time I parked, however this was not a good solution since you need chasis battery power to run the dash radio/CD player, slides, step, or even start the generator - which even if you did start the generator, it wouldn't charge the chasis batteries back up!
What is supposed to happen is that when the Xantrex inverter charges the house batteries up to 13.5 volts, a solenoid diverts current to the chasis batteries and charges them. Apparently this works fine in Washington state, but in hot moist climates like Florida where I live, the temperature sensor never lets the house batteries get above 13.4 volts so the solenoid never fires and the chasis batteries never get charged.
The 2005 models do not come with an echo-charger. The dealer finally got permission from Western RV to install one (it turns on whenever the current to the house batteries is over 13.0 volts) and this should solve the problem