Hi Simon
It sounds as you have two issues
1. Low Batt warning
2. Pump pulsing in/out of DE
The controller you have is about 2 years old. The controller measures voltage at the control. Volt drop along the length of the cable will mean that the voltage shown at the controller will be lower than at the battery for example the battery nay have 11.7V the controller might see 11.4V.
1st check the cables and connectors replace any worn cable or rusted connectors. Also ensure the cable is as short as possible. ( Longer cable means higher volt drop )
Turning the controller up high draws a higher current (amps) from the battery the controller will see this as a sudden spike of power this may momentarily drop the voltage below 11.5 at the controller.
The controller is sensitive to even voltage change even for a fraction of a second and will flash Bat.
2nd the pump pulsing may be associated with the same volt drop issue due to the way the controller senses stopped flow.
I would also suggest you recalibrate the controller using the auto cal function. Have a look at the video link
http://www.youtube.com/watch?v=9kKoskb7l7c&list=ULYou also mentioned the problem has been happening for a few months. Did you change any fittings, different size hose or replace the pump? at the time the problem started?
Hope this helps, let me know how it goes
Cheers
Ian