wayne said,
"I'm seeing about a 0.6 volt difference between the battery and the controller with 3.5 amps flowing. That is a bit more than I expected."
That is excessive voltage drop for only 3.5a. For example, I see .09v (point zero nine) drop at 45a. It may be simply a disagreement in meter readings, between the controller's display and whatever you used to read voltage at the batteries? Confirm all readings with a single handheld meter, to be sure.