Why do you think converter is not charging batteries while on generator power?
Is this something that has just happened?
Are batteries currently being charged?
Reason I ask is......
If everything is working via shore or gen but last time you used gen batteries didn't charge, have you tried shore power since and do batteries charge now?
Unless battery disconnect switch was turned off, circuit breaker for converter input is tripped or reverse polarity fuses on converter are blown, either AC power source can charge batteries. Either both work or neither work.