I hate to ask you a question in response, but is your electric choke working properly?
There is a secondary valve lock-out lever feature that is designed to work while the choke still warming the thermostatic spring. It prevents the secondary system from engaging while the choke still on.
This is just an educated guess, since I am more confident about Holley carburetors than Q-Jets (and I had E4ME overhauled for me,for I did not want to experiment with my original L81 carb).
Perhaps JohnZ, Jack, or Stingray6974 (Mike) can chime-in on the subject and volunteer possible explanations to your question.
Your adjustment is wrong, the secondary throttle plates should start opening at about 40-60% throttle, and arrive at 100% open at the same time as the primaries. Now if you are talking about the secondary air valve (the butterfly on top of the secondaries), that should not open at all by opening the throttle, engine running or not. The air valve opens by engine demand (load) so you would never actually see it open unless you are running down the road with no hood or air cleaner. God bless, Sensei