guvnor
There's more behind the scenes stuff that you, and others here, will never know about. The AA folks on here will hear about it through other channels. (Clue, AA supported the Captain's decision).
Fair to say though that if one can't "find" the agent in the terminal (and make full use your alleged 75 minutes between departures) for a pre board check, an announcment along the lines "Would the secret service agent travelling to Dallas, continuing on to Waco to guard President Bush, please make themselves known to the gate agents at gate XYZ to complete new paperwork" may not necessarily be in their best interest.
Too bad you keep calling for the race card. I do not know the Captain personally. You are mistaken to second guess him/her, unless you have walked in his/her shoes (notice how you ASSUME it's a HE!).
Bottom line, if the paperwork DOESN'T jive, the first thing the FAA says at the hearing (assuming one makes it that far) is "Why did you depart when the paperwork clearly was incorrect?".
Guv, you can pontificate all you want. It seems this WAS a genuine SNAFU. The benefit of any doubt should fall to the Captain. Remember, the Captain responsibly flew over a hundred people, SAFELY, to DFW.
At the time, the SS agent understood "it was nothing personal".
When you start to run your airline you too will discover that nothing's ever quite as starightforward, or black and white, as it seems.
Happy new year.
ps AA folks should realise there's more to it when "AA supports its Captain!".