Hi Steve
Thank you for the additional information. You likely have a V9 controller which were produced up to November 2012.
I am basing the comments below on the assumption you have a deep cycle leisure battery.
A car battery has different discharge characteristics
Now the V9 measures voltage at the controller so dependent on the length and condition of the cables you may see a different voltage at the control and at the battery if using a hand held volt meter.
A 100 AH battery running your pump at a flow of 86 means you are likely drawing 4 - 5 amps an hour now assuming your battery is 100% charged at the start of the day with 13V or more You can expect 8 - 10 hrs work to run the battery to 50% capacity or 10.5V as recommended by Battery manufacturers.
http://www.progressivedyn.com/battery_basics.htmlI feel you are seeing two effects
1. The battery is not holding a charge as well as it used to
2. Volt drop along the cable
Have a look at this link
http://www.springltd.co/node/133You will tend to get quite a rapid and sudden fall off in the battery as it loses its ability to hold a charge.
The controller is sensitive to quite small changes in voltage. This could mean that as the battery charge falls the pump will want to pull more current to maintain the flow rate this could lead to a sudden drop below 11v. Even if this drop was for a second or less the control would see the drop and stop the pump.
Once the pump is stopped drawing current the battery voltage will recover. The control would not instantly restart the pump.
I would suggest a long bench charge to get the battery up above 13.5V ideally as close to 14V as possible and then see what happens
Charging a battery to near its maximum will take some time possible 24 - 36 hrs. If the battery still falls away quickly then replacing it would be the answer.