Try it with a resistive load instead of the battery (say, four 12v car headlights in series, or a 115vac 500-1000w halogen bulb). I would bet that it starts up fine with the load connected first that way.
If it does, then it means that something is going on with the voltage detection of the output stage, and it isn't allowing it to startup because it thinks it already *is* started up.
If you put a diode (that can handle the full current and power dissipation needed for your setup) on the output of the MW to the battery, it will prevent the MW from seeing any voltage there and so it would then start normally, if this is the problem. This complicates the final full charge voltage setting of the MW a bit, as the voltage drop on the diode varies with current (as current drops, the voltage drop decreases, but there will be a minimum amount of voltage drop you'll need to adjust the MW voltage up to accommodate).