To be honest it can very well be those wingnuts that are the cause of your problem. (which is why I was specificly asking if you were using those or not).
Wingnuts do not provide a good connection to the battery, and they will come loose on the battery. What happens when the engine is up and running is that the alternator will see an intermittent connection to the battery.
Think of this like it was a little kids game, as your running down the water the battery tells the alternator "now you see me, now you don't, now you see me, now you don't" just like a kids game. What happens is this causes the voltage to spike inside of the regulator portion of the alternator because that voltage needs to go somewhere, and if it can't go anywhere because of an intermittent connection, the regulator portion goes up in smoke, and the alternator no longer works. It's a very common occurence and I run into to a few times a week.
The fix is to simply get yourself some stainless steel nylon locknuts from the hardware store along with some lockwashers. Sand down the battery cable crimp ends so that they are spit shine clean. Clean up the battery posts. And reinstall the battery cables with the locknuts. If you have a few wires going to the battery for other accessories, make sure the main battery cables are the wires on the bottom, directly on the battery posts, and not stacked on top of other wires. Also make sure your battery box is secured to the boat, and not sliding around. But it's those wingnuts, as simple as it sounds, that is the root core of your problem here. I have a toolbox drawer full of them.
Feel Free to post back with questions