Couple of interesting things....

[Isaac-1]

True, but the original poster is likely not talking about drained batteries which have a higher charge acceptance ability, since his system was raising not lowering charge voltage after several minutes of operation.

 

[rustystud]

You can still cook AGMs.

I have never seen a cooked AGM, but what I have seen is a battery with a damaged case that seeped out fluid fry. What usually happens with our batteries is the cases get damaged, there charged (with the factory chargers) and because fluid loss has happened, the battery vents get blown out rather dramatically !

 

[Chainbreaker]

Some good battery charging info here:

http://batteryuniversity.com/learn/article/charging_the_lead_acid_battery

By the way, if it were me I and suspected a charging/battery issue I would first disconnect and charge up EACH battery independently with a 12 V charger and after charging let the batteries rest overnight disconnected from one another. Then check each battery independently as to voltage reading to determine whether each battery is good/marginal/faulty. Then you know the state of each battery and can go from there and measure the output of the genset VR connected to known good batteries that are already at full charge voltage to determine whether there is an overcharge situation or not.