Flight agent wouldn't let me check legal setup. Advice?

The basics: I fly a lot for work, and I have LTCs in multiple states to cover as much as possible. The hubs and I train as much as possible and keep up with the laws wherever we travel. So, in at the airport and I went to check my bag and declared the firearm. The person was very kind but new so she grabbed her manager. It was unloaded in a Pelican case, with the ammo out of the clip but in its own little section (pluck and pull foam is awesome). I've done this multiple times and never had an issue.The baggage agent manager refused to let me check it, and when I asked what the issue was, she wouldn't answer and called airport security. Again, I asked what the issue was and she told me that the ammo needed to be in its own locked container (essentially a second Pelican case). This is not true (according to tsa.gov, it can be in the same case). I showed her the website excerpt but that wasn't going to change her mind. I didn't want to make a scene, and still had a plane to catch, so I said I'd call my husband and have him come back to pick up the ammo. She tried to keep my gun and I said absolutely not, re-locked and took the case. She had the security guy wait with me until I walked outside to meet my husband, and still didn't want to check it when I came back. Now, upon trying to check in for my return flight, it's been flagged and is giving me a message to go to the ticketing office because I have a firearm (this is new, I haven't seen that before).So here is my question: what, if anything, should have been for differently? I try very hard to give gun owners a better name and to do these things fairly subtlely. I'm not sure I handled this as well as it could have been, but I'm at a loss for what could have been done better.. I didn't want to make a scene but I was completely legal in what I was trying to do, and she was ready to call the police. I was able to just have my husband come back, but that won't be an option if this happens when I'm checking in for a return flight. Should I email someone from the airline to let them know what happened? Or is there a better route for handling this? via /r/CCW https://ift.tt/2EenLkn