I am dealing with the same issue right now! Actually, I have been working on it since last October! I did the MAD bypass and my head lights started strobing. I was stumped.
I am going to rewire my MSD 6AL-2 tonight to be temporarily powered by a separate battery (not powered by my car) and see if it makes any difference. From there i am going to start rerouting the wiring to see if I am getting interference. I have gone over EVERYTHING since last October and can't find any corrosion of poor connections. I was starting to suspect the MSD box but... now I am fairly certain after googling the issue. I will post an update tonight.
