I was looking at the symptoms and thinking that the alternator may not have been connected to the batteries during run condition, so both batteries, or possibly only one, were powering the amps AND the ignition and everything else for as long as they could. Just the amps, probably a heck of a lot longer than 30 min, but fuel injectors and computers and spark plugs and all those damn sensors and servo driven gauges and electric fuel pumps, ballast pumps, etc. hair dryers, tube blower uppers, dvd players on the tower
, etc. use a lot of amps. He said that he took the boat out for a run, (how long?) and then parked the boat and ran the stereo for ten minutes. After that, it wouldn't crank. If the batteries were combined via the isolator and weren't getting charged the whole time, they could both have been drained. If the relay isolator was energized while running with or even without an alternator charge input, and one battery was dead, the good one could have discharged into the dead one, resulting in two mostly flat batteries relatively quickly, that's why diode isolators can be useful, they wouldn't allow that cross charge to take place, they are one way switches. Relay isolators and mechanical switches are cheap and work well but should't be used when combining dissimilar batteries, i.e. deep cell and starting battery. If the stereo was running when the boat was parked, was the isolator powered up and combining the batteries? The isolator should turn off when the engine is not running, and not be energized in the "accessory" position if the aux battery is supposed to be isolated.
Easy to troubleshoot, start the boat, check the voltage on each battery, should be pretty close to equal to the alternator output and more than 13vdc. If one battery is not, charge it for a while with the engine or a charger, and check again. Turn on a load like a ballast pump or stereo amp, the voltage should drop a little but not below 12vdc or so, both batteries. Check the voltage drop across the contacts of the relay, it should be virtually nothing, way less than .1 volt under load. Kill the engine and the isolator should deenergize, disconnecting the starting battery. Measure the voltage from common to each side of the isolator. The voltage on the aux battery should drop a bit when you turn on pumps, etc. The voltage on the starting battery should stay the same, and remain higher than that of the aux battery. That means that the isolator is doing it's job. Relays will still allow bad stuff to happen when one battery or the alternator fails. Diode isolators will cause batteries to fail over time due to undercharge, and use up a lot of voltage to turn on and off.
HellRoaring isolators use a solid state relay, they combine the best features of both types of isolators, one way energy transfer and very low voltage drop, so no battery damage. They are expensive (140$) but so are my weekends! I don't sell 'em or anything, I paid retail for mine. Heard about them here on Wakeworld.