So... you have the charging lead from the engine going to the battery switch, then individual cables from the #1 and #2 switch positions to each battery, right? With the switch on a specific battery, you're getting full charging at that battery - no need to disconnect anything. And, with switch on #2, you're seeing about 13.5V at battery #2, but with the switch on #1 you're only seeing battery voltage? What is that battery voltage at each battery with switch OFF? If both batteries are good (load tested?)... Either swap the batteries or the cables and see if the problem follows the cables or stays at the battery.
Are the grounds good?
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Checking F150TXRD charging output
I can't get my #1 starting battery to charge properly. It is 6 months old. I have two batteries and a typical 1-2-both switch. I also have hooked up isolater run from engine to #2 battery and that seems to do the job for that battery. All battery cables replaced last fall. I want to check the charging output without interference from the battery being under-charged. I am assuming I could start and run motor with battery switch set to "2". Then disconnect red and black from #1 battery and check with meter. That should give me the true output from motor to battery, correct?
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