"Is it possible for the converter to charge the house batteries thru the generator but not thru shore power?"
The converter does not "go through" the generator. The generator, when on, provides AC 115VAC directly AND 12V indirectly to recharge the batteries. On my Vegas model, The converter uses the 115VAC "shore power" to generate the 12VDC to recharge the batteries. The schematic may be different than the one shown that has a separate generator output and a full wave bridge rectifier (diodes) that is connected to the house batteries. When the shore power is connected, the output of the 12V converter is regulated to provide proper high charge rate and "float" charging to the batteries so that they do not get overcharged and damaged. If the generator is used to charge the house batteries without regulation, overcharge and damage is probable. If the generator is supplying 115VAC and the batteries are not charging, the converter, supplied by the generator 115VAC, is probably not working. Check your particular schematic to see if it is using a separate output from the generator through diodes to charge the house batteries.
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