Originally Posted by LiquidForce
From my point of view it looks like one of the batteries is shot. The battery isolator ensures the separation of the two batteries. If it is a simple diode then you will have a voltage drop between the in- and output of usually about 1V which about matches your measurements. There are slightly more expensive solutions on the market like the "Sterling Power ProSplit R" I'm using with zero voltage drop.
Now when you bypassed that isolator your two batteries balanced, meaning the weaker battery drained the better one until they were even. That is why I think one of your batteries is causing the issue. The good one has a rough life supplying the weak one and all the other drain you put on it. Try measuring the voltage on both batteries when putting load on them. If one of them drops significantly you know where the problem is. Measuring the batteries with no load has no point, a close to dead battery will be happy to show you 12 to 13 volts in idle.
Edit: Forgot to mention: Measure the batteries independently from eachother. Measured with your bypass will give the same readings for both batteries since they are connected.
actually i just connected straight to one battery. Got it into the shop today and there was 6 tach fault codes. They cleared them and could not replicate the problem in the shop. next step is take it back to the lake and if it happens again they will come to the lake to do a water test.