LM339 Incorrect Behaviour for Two Elements
Well I feel silly now. I've found the problem. My prototype PCB had the wrong two pins on the pots shorted so I had cut the traces and shorted the wiper across to the other pin. Due to the way the board was laid out the BatTap and PanelTap are run from different places and I didn't realise that BatTap was now connected to the wrong pin of the pot after the mod. So the voltage I was measuring for BatTap was not actually what the LMV339 was getting. What led me to the solution was wondering if there was a poor connection on the BatTap line that was causing increased resistance in that line.