...not to mention "common sense", for that matter... (grin)

Really appreciate your taking the trouble to address this, but my setup as is definitely is reading each battery independently... Just confirmed this yesterday, after the starting battery was offline from the charger for awhile. When I re-connected it, it was clearly indicating a different state of voltage from the house bank...

One point... This setup is using what Xantrex refers to as a "Dual Shunt", in case that's different from what you are picturing...

I should note that I really only use my Link 2000 to measure voltage, and whatever amperage is going into the batteries from any charging source, or amperage being drawn when not being charged. I've never bothered trying to calculate or keep track of Amp Hours, an accurate measure of voltage alone is good enough for me...

The only diagram I can find is posted below (don't have a scanner, so I can't duplicate the one from my owner' manual. And, for some strange reason, the current Xantrex Owner's Manual pdf available online doesn't include the wiring diagram mine has)

This diagram is only for one battery. The one that shows two batteries, has the negative of the second battery connected to the same spot on the shunt that the negative from the solar panel goes to in the diagram below. And, for whatever reason, the diagram for the 2 battery setup has the position of the YELLOW and BROWN wires going from the monitor to the shunt reversed...

Confusing, at least to an Electrical Dumbass such as yours truly... (grin)