The manual I referenced above covers all variations of the Pathfinder. 100/3 is the 100A, 3 bank version and it can do 12v or 24v. Do you have a different manual for it?
The way I read it, the red light says the High Voltage Disconnect threshold has been reached and charging is discontinued. I don't see any mention of a high battery temperature, or any means for the Pathfinder to determine battery temperature.
From what you describe, the problem is in the inverter battery bank, i.e. the red light comes on almost immediately when that bank comes online. Are they flooded cell batteries? If so, remove the caps on the cells and make sure each has electrolyte 1/4" over the tops of the plates. Add distilled water if needed to bring the level up. If some were low, give it another try after adding the water. What happens when you turn the inverter on - does the battery bank power it ok? Or does the inverter cut out on low voltage?
Beyond the above, you could probably take the batteries out to a shop that sells batteries and ask them to do a load test for you on each. It's free in most places. One or more batteries may fail the test.