Starter Battery/Alternator Issues

[B-to]

Would like some advice on possible issue with my alternator and starting battery.

I have a 2006 Dufour 34P with two house batteries and one starter battery. The alternator has a positive charging cable going to a multi-battery isolator. From there smaller wires go out to each of the positives on the house and starter batteries. Running alongside the positive charging cable from the alternator to the isolator, is a smaller red cable that seems to have become disconnected from the alternator (it has a small, two prong plug connector at the end near the alternator that is not connected). There is also a yellow wire near the alternator that seems to also have a female two prong plug, although it doesn't seem that they fit together. Tracing the red wire back it appears to go into fuse box and then to the Isolator (but that could be wrong - hard to follow). Does anyone know what that wire does?

Recently the wire from the isolator to the starting battery completely fried and starter battery needed to be jumped. The marina installed a new wire but did not diagnose the cause.

This weekend, at rest all batteries measured 12.42 on Volt Meter. When starting the engine with revs at 2200, starter battery is only charging at 12.92 volts and the house batteries are charging at 13.46. Is this sufficient to charge the starter and what could cause the difference? Could it be the disconnected disconnected wire (but that should effect both battery sets)? What could have caused the starter battery wire to fry?

Any thoughts/suggestions appreciated.