Iíve noticed with those small auto chargers that itís common to get an error when charging dead batteries. Usually itís because the battery is gone or youíre starting off on the higher setting like 10 or 12 amps. Try to start off at a lower setting and once the battery voltage begins to rise after a few hours then ramp it up to high.
As far as the Xantrex, I have the Prosine 2000 and it will charge the chassis and house systems but each model is different. The Separator must be in the closed position. If you lost both battery systems it sounds like the separator didnít operate correctly (provided you have one) and something killed everything. Also you might have an isolator which SMB quit using and replaced due to problems had with them. At any rate you must track down what killed your batteries in the first place after you get the batteries back up. Itís possible you have a bad battery, so during the charge go out and feel the battery box. If it gets hot (not warm) stop charging and pull the battery. You should always replace both starting batteries if one is bad provided you have two starting batteries.
Besides the FAQ's here you can find some other info at this site:
Good luck and post back on what you find