"Why would the controller show 14.1 volts for the batteries and I get a reading of 13.4 volts when I check at the batteries?"
Assumes you have tried your meter against another meter or known voltage so it is not "reading low"
When there high resistance between controller and battery the controller thinks the battery is higher voltage than it really is. The controller starts "controlling" at a voltage set point of say 14.4v. So when it sees 14.4 it starts controlling and the battery can't get any higher in voltage---and it is really at some lower voltage than the 14.4 it was set to be at. So the battery will be "undercharged"
That is why all the fuss about getting the controller-battery path's resistance down. You can shorten the distance or fatten the wire or do both. Or the wire might be ok and it is a poor connection.