It doesnt sound like you did this, but if you unscrew the adjusters on the mbc, the springs can pop out without you even realizing it. This happened to me once, i unscrewed the knob on my xbc all the way and the spring popped out and I didnt even know. Next time i floored my car I almost shit my pants when it spiked to 28 psi. another thing that can happen is the springs get caught up on the threads inside the mbc causing the adjustments to not affect your boost. Slowly loosen the bolt on the mbc being careful not to let the spring pop out and then check that the spring isnt stuck in the mbc. Also check you electrical connections on the dual stage controller, maybe the actuators in it arent working properly. I am pointing all of my fingers at the mbc after all of the tests youve done.