It sounds like when the generator was repaired that it wasn't wired back up correctly. I don't know the details of the MS2000, but a backfeed error would suggest that the outputs of the MS2000 and the generator are connected together, which they should never be. The gen output (and shore power) should go to the MS2000 AC input. The loads are then connected to the MS2000 AC output, and anytime there is power on the input side it gets passed through to the loads and the charger
I don't know the nature of the generator repair and whether this is plausible, but it's worth consideration. It would explain the symptoms that you describe.
Also keep in mind that there are lots of different bypass and selector switch possibilities that your boat could include as well which would complicate things further.