The low battery cut off disable will stop the controller shutting down the pump if it thinks voltage is below 10.5V But the controller will continue to monitor and display information on the battery.
Volt drop could be an issue. Although copper is a good conductor it is about 80% efficient so some volts will be lost along a cable length. Keeping cable runs as short as possible will help also ensure all connectors are in good condition including the fuse and fuse holder. Corroded or damaged connectors will get hot and reduce current available to the pumps.
Another issue could be battery size, runing two pumps a 110 AH is probably a good idea. The original post does not mention if the battery warning is at the beginning of a day or during. If you find that after a couple hours the warning comes on and voltage falls it may be a sign that the cells are not holding a charge or possibly the battery is not getting charged often enough .
Most batteries you can drain to about 50% of capacity below this the lead cells even in a new battery will degrade and not hold charge as well. Two pumps are going to draw 6 to 8 amps an hour with a controller. An 85 AH battery will have 42.5 amps of usable energy so between 5 to 7 hours before it will need charging.
http://www.progressivedyn.com/battery_basics.html