I think Hans was referring to the same thing but some chargers aren't good at dealing with conflicting charges on the same battery/bank. This is most typical when one of these chargers is hooked up to the generator battery. When the charger is operating with the generator running, it sees a conflicting charge from the generator's charging system. This drives some charging computers nuts and will shut down that particular charge leg or all of them depending on the charger. Some chargers aren't affected by this at all. The remedy is to disconnect the charger from the generator battery or install a switch to shut off the charge to the generator battery when you run the generator.
If your charger is hooked up to the generator battery, try disconnecting that leg then run the generator and see if the charger still acts up. If it works properly, don't hook it back up, the generator is capable of maintaining its battery on its own. The caution here and with installing the switch mentioned above is that some chargers need ALL outputs hooked up. If yours is like that, just hook it up to another battery or jump that output to another one at the charger output bar in the charger.
This is all assuming your generator is outputting properly, both voltage and frequency. I've always said every boat should have an on-board frequency meter. These have gotten very affordable and come in handy to monitor marina output as well as your generator. There are digital units you can install in your electrical panel that will also show other info like voltage, amps etc. or ones that will plug into any outlet so you can monitor power quality.
This is an example of what I'm talking about:
https://www.amazon.ca/Yeeco-Digital-45-65-0Hz-Frequency-Voltmeter/dp/B01ER5DWDU/ref=sr_1_21?s=industrial&ie=UTF8&qid=1526004979&sr=1-21&keywords=frequency+meter