Open collector logic question
If they are open-drain lines during initialization and they are pulling high then try a 1k pull-down resistor so that the 1k resistor wins the battle (after all it's probably only fighting against a weak pull-up during initialization). You need to check this.

After the unit has initialized it can drive the line (and transistors) and operate correctly. 

Are you putting a resistor in series with the base on each transistor. Something like 1k should be fine.