Effect of batteries in a solar pump system

After running a solar pump system on my ranch for a couple of years I decided to look into putting some deep cycle RV batteries in to, hopefully, get an extended run time out of each day of pumping. After doing some research and continuously "rattling the tree" of the techs from the company I bought the system from it was finally admitted that, #1, the controller/regulator runs the pump off the batteries ALL the time when there are batteries installed and, #2, this results in a 15% to 20% reduction in the daily water production due to the time it takes to charge the batteries back up in the morning.

This seems completely backward to me as I thought the batteries would be charged during the day and discharged after the Sun no longer gave enough light to produced power through the panels. Is it normal for solar pump systems to work like this?