Keep pursuing the matter with the higher ups at the TSA. I had a similar situation in which I almost got arrested. I called, e-mailed, and snail mailed the TSA "customer service" people and got a letter which I carry around in my bag from the director of the TSA at JFK which says something like any crew member is allowed through a security checkpoint with a valid air carrier ID badge. The only exception is if a terminal in strictly for international based carriers. Get a direct phone number to someone who has a little bit of power.