Since it's your cranking batteries that are low, I doubt that they charge at all from your Xantrex charger. Usually the cranking (or chassis) batteries are isolated from the coach house batteries on the motorhome. It is the house batteries that are charged by the inverter.
You may have a separate Trik-L-Start battery charger designed to provide a low amperage charge to the chassis batteries when plugged in. I don't recall the exact year Winnebago began installing those, but someone else with an '04 should know if your unit has one.
If you don't have one now, it might be worthwhile to add the Trik-L-Start
to your rig to compensate for parasitic battery loads on the engine batteries.
Joe & Shelly, Justin, Tyler, Alyssa | Butler PA
2008 Tiffin Allegro Bus 43QRP|Cummins 425|Honda CRV