Mytlamb -
Your voltage of 11.7 VDC is way too low. It represents a fully discharged battery, though of course without any further info, I have no idea why it is discharged. It sounds like your converter is trying VIGOROUSLY to charge this dead battery, and you can't fault the converter for this.
Caver's suggestion of a shorted cell sounds good. When you measured the voltage, did you measure it while there was a load on the battery? This may be the only way that the problem shows up as a voltage measurement. Disconnect shore power, and turn on a bunch of interior light - then make the measurement while they are on. Wait five minutes, and make it again. Are the battery voltages still equal?
Unfortunately, I don't think that turning off individual circuits will help you. The problem as described is in the battery, not the circuits. If there were a bad circuit, the converter would try hard to power that circuit, and might blow the fuse associated with that circuit - but the excess current wouldn't pass through the battery fuse.
Finally, it was a good idea to replace the original glass cartridge fuseholder with an ATC automotive fuseholder. The glass fuse holders are famous for overheating and melting the plastic, even in the absence of a problem. An ATC fuseholder should not overheat.
Let us know what you find.
Bill
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