Well, if anything it would be the black box causing you problems, not the map sensor. Atleast under boost. Because if it is a voltage clamp, then it clamps the voltage of the stock map sensor so that it doesn't see boost, like you said. If your ecu did see boost, then it would throw the car into limp mode...or atleast that is what I have read.
What are you using for fueling? larger injectors or rrfpr?