I think at least some of the Magnetek 6300 series had a sort of internal transfer switch arrangement where certain circuits were connected to the 12V battery (presumably those that needed "clean" DC power) and others were switched between battery and converter power by a relay. This means that the DC distribution panel has two supply busses. With a more modern converter/charger, these should all just be connected together to form one bus.
It sounds to me like probably your (former) switched bus isn't connected to anything anymore.