Nova,
I don't have an answer as to why you are having your problem but it sounds like you are stalling the fuel in the lines. The bypass could have a problem when you take of there is a spike in fuel flow resistance and it sounds like the pump is giving up at that point. I would call aeromotive and see what they suggest or pull the pump apart yourself and look things over.
One thing I just thought of though you said the pressure on your data logger shows zero until you let up on the throttle, is that at the end of the pass and the carb did not run out of fuel? If so it might be a sensor problem. Just some thoughts.
Curtis