Doesn't surprise me. While I've never had that experience with a Federal prosecutor, I have had to educate a Judge or two on a variety of drug laws. The first time I was surprised but a prosecutor friend told me something I've never forgotten. Just because they're a judge does not automatically mean that they know the law. Scary but true. And as we all know, more then a few ATF agents are fairly ignorant when it comes to firearms (espicially the NFA stuff)
In any event, hopefully, your session with the Fed showed him the light. At least you have a good enough rapport with him to where you can sit down like that and explain things.