I flew Air Tran from ROC last Saturday AM
Brought two pistols inside a hard pistol case that requires manual dexterity to open and it was placed inside a locking, hard sided suitcase. Also included inside the suitcase, but not the pistol case were two loaded Beretta mags inside a Bianchi pouch that covered the magazines, and one "loose", loaded magazine, plus two loaded 1911 mags with bumpers, inside a pouch, and two paper boxes of Remington/UMC ammo .
1) To the counter: "I need a Firearms declaration"  "OK,  may I see the guns?"  Opened and demostrated that they were indeed unloaded, filled out the declaration, and stepped over to the TSB contractors, here's where the fun begins.....
The agent couldn't open the case and they couldn't let me do it, finally I talked him thru it and he got it opened.  Then he started giving me a hard time about the loaded magaziens, I assured hin that it was perfectly acceptable to ship them the way I had them.  (I do hold a Hazardious material shippers certification that included commercial aircraft)  he continued, and encouraged me to take the ammo back to the car (couldn't becasue I was dropped off at 4:00am)  Finally he called a supervisor, who proceeeded to tell me that ammo could ONLY go in its original packaging and told me to take it back to the car... finally she called over someone in a sportjacket who looked over the deal and said " I have no problem with any of this except the one "loose/loaded" magazine.  "OK" I said, I go thru 10k of ammo a year elevin rounds ain't gonna change a thing in my life, call over a partol.  Fifteen minutes later a Monroe County Deputy shows up, the situation is explained that I want to dispose of 11 rounds of ammo. He unloads the mag, tosses it back in the suitcase and starts to leave when the Supervisor asks if he wants here name for the report (he didn't) but decided he'd better take down everybodys info, then leaves and so do I
There was an issue with the pistol case not having a key/tumbler lock.  Cleared because it was inside a locking suitcase. (but they didn't want to do it)
When I challenged the supervisor to produce the IATIA manual (regulations for transporting hazardious materials on commercial aircraft) she couldn't, hell didn't even know what it was.
She tried to blame the airlines saying that those were "their rules" not knowing that each carrier has its own rules and guidelines that all conform to Federal regulations.
Pointing out that the ammo inside the mags was not only leagal but more safe and secure than using the paper factory boxes fell on deaf ears.
Bottom line is this: Know what you can/can't do.  Stick to your side and go overr the supervissors head when they obviously don't  know or won't do what you know is right.
I did capitulate and empty the "loose" magazine, in all fairness it should have been stowed better, but in the past they have gone un-challenged.
Good thing I arrived early and they weren't screening a lot of bags becasue I tied up four ass-clowns for almost a half hour...oh well, that's what you get for trying to be a prick on a power trip to me at fourthirty in the morning.  
YMMV

Sounds like a PITA, glad you got your flight.

Quoted: She tried to blame the airlines saying that those were "their rules" not knowing that each carrier has its own rules and guidelines that all conform to Federal regulations. The airlines regulations can NOT be less than federal, but can be more strict! Pointing out that the ammo inside the mags was not only leagal but more safe and secure than using the paper factory boxes fell on deaf ears. Federal regulations require that loaded magazines must be securely stored inside of another container like a mag pouch. YMMV

I can not wait until I travel again and quote chapter and verse of their own manuals!

Bill H.