The problem will not be down to battery voltage whilst cranking. I don't know what version of software your MS uses but the one I've looked through has voltage compensation for the injectors allowing for a range of 7.2 to 19.2 volts. I cannot imagine any ecu not compensating for variance in battery voltage otherwise the ecu could never deliver it's fuel accurately.

If the injectors aren't firing, have you checked to see if the MS is getting the crank position signal?