Sure, why wouldn't they? They have no-fly lists. Why wouldn't they have "difficult passenger" notation in the passenger record?

Every business has customers who are more trouble than they are worth, and should be fired. Back in my marketing director days, I used to say that I was doing myself a huge favor by handing a business card and sales brochure from the competition to certain problem customers.

My best suggestion is to get the name of the highest ranked person you can find and write a polite, succinct email to that person stating your case as nicely as you can.

Remember, however, you did not discover the "error" until after you talked to the first agent. By your own admission, you were wrong and the agent was right, based on information available at that time.