Battery connections

If you leave the charger always on, it is essential that when it reaches about 13.6 to 14.0 volts that it switches to float charge.
I suspect that your charger basically cooked your batteries

The mastervolt is a good charger I am told. I was told to leave it on by the makers. But it does not account for a duff battery, which was my problem, it's been fine since charging just two batteries, the faulty one is disconnected.
 
The temperature coefficient of lead-acid voltage is negative, so the hottest one will draw the most charging current and get hotter.
I would test each battery by isolating it and charging it alone, then discharge it into a load of 10amps or so for an hour to check it has some real capacity. If one battery is badly mismatched, the volts will be very different from the other two.

Possibly worth checking electrolyte gravity while you are at it, one battery/cell could have suffered acid loss at some point?

If that's a sailing or offshore boat, the batteries should be bolted down, not just in case of a knockdown, but also to avoid stressing the connections every time you tack. They can work loose in time.

Come to that, the heat could have been generated in a bad connection?

I think at least 20% of the energy put into charging is lost as heat. That has to go somewhere! Modern batteries do not have the mass of lead like old ones of the same size, so get hotter if there is no cooling.
 
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