That particular controller looks as though it can do charge control or load control, or diversion control but not charge and load control together - if you want to do low voltage load disconnect you would need two; one between the panel and battery for charge control, and the other between battery and load to do LVD.
Have you set the dip switches on the controller for 12v battery? By default they are set to autodetect, but if the battery voltage is outside the expected voltage range the controller can't determine what voltage it should be charging to. This might cure your problem of starting with a dead battery but I'm not sure - most controllers assume you never let the battery drop too low (as damon said, it kills the batteries quickly).
One possible solution:- This controller can be setup as a diversion controller. For this you need a dump load (big resistor/heating element) that can absorb all the current your solar panels can produce. You then connect the panels directly to the battery, and the diversion controller regulates the battery voltage by turning on the dump load when the battery is full. In this setup, even if the battery is dead, the solar brings it back up, and the charge controller doesn't have to do anything until the battery reaches 14v.
Is your battery lead acid? or lithium which might have its own management system and disconnect itself to prevent overdischarge?