Thanks for the answers. When I started up the generator, I heard the ATS click in and I had 120v power in the coach. When I hooked up shore power before I turned on the generator, I did not have 120v power in the coach. However, when I just hooked up shore power again to check, I now have 120v power and shore power is charging the house batteries. It may be that the ATS did not switch to shore power the first time and turning on the generator somehow unstuck the ATS. Whatever, that problem seems to have solved itself.
The other issue of the alternator not charging the house batteries is almost certainly an issue with the battery isolation system. These Class Bís do not use a BIM or BIRD system, but just have a battery manager hooked to a solenoid which only operates one way - alternator to house battery. Shore power/generator does not charge the chassis battery. Winnebago also uses three circuit breakers between the battery manager and the two batteries and voltage wire. I have not liked this system - it has five points of failure as well as working only one way. So I have purchased a BIM 225 that will replace all five components and charge both the chassis and house batteries on alternator, shore power or generator. I hope it solves my problem - now that I am back down to one.