Hi Rich
Depending on the version of controller is in use low battery warning would flash at
V9 version: BAT displays if detected volts are 11.5V or less. Pump shut down at 11V
V11 version: BAT displays if detected volts are 11V or less. Pump shut down at 10.5V
The V11 also has a low battery cut off, Over ride feature.
https://www.youtube.com/watch?v=3u2-5R66GcA&feature=youtu.beThe two versions also measure voltage in a different way. The V9 is measuring volts it see,s at the controller.
The V11 is actually measuring volts at the battery, This makes the V11 more accurate and nore efficient. The V11 is more efficient at returning unused current back the the battery.
Referirng to Dons initial post I would agree that a loose connection and or worn fuse holder are the likely source of the problem.
Both V9 and V11 are quite sensitive to small changes in current even when the current change is only 1/2 a second or so.
So as the battery comes under load volts dip If this is combined with a faulty connection the dip would be enough to cause the control to flash Bat
As load levels and the battery recovers slightly to come above the warning Threshold the control will stop flashing the BAT message after a short time.
The suggestion of good battery terminal as opposed to croc clips is a good idea