Is the pain only in your rear ankle?
I have single BOA and get the exact same pain that you get. Right on top of that ankle bone. Only in the rear ankle, though.
I kind of diagnosed the problem as being from the nylon strap in the liner being pressed on by the overlying BOA lace when the boots are tightened. I have tried breaking my boots in to the max but nothing helps. I can't even walk in the boots anymore because of the pain.
My only choice is to go to the Burton Zone lacing boots for ease of tightening, but I sure as hell am going to miss the simplicity of BOA. I think BOA is by far the superior system for dialing in and adjusting your boot preference.
Let me know if you discover a cure besides an ankle pad.