It really sounds like the battery to me. When it runs down can you attach you system to your van battery? I can do this with some elongated wires I have.
If it then works fine, you know the fault is definitely with the batteries.
I'm no expert though.
Oh, one thing that happens with my system is that I have a two man system, two pumps and two flow controllers (one flow controller is from cleaning warehouse and the other I can't remember - but they're two different types), and when my battery is low, the pump attached to the cleaning warehouse flow controller works great, but the other pump attached to the other flow controller doesn't; it stops with a "L" flashing (I guess it means 'Low Battery'.