I ship comics ALL THE TIME using media mail, and never had a problem. However, learning of your post, I just asked the wife and she says, technically no, they are not allowed. She says the reason they are not allowed as "media mail" is they contain advertisements. I even asked her about magazines and she said the same thing. "Nope. They have ads"
She also doesn't agree with that "rule" as older books have ads in them all the time but they allow those it seems.
Sorry you got "pulled over for it", my man. I never even gave it any thought.
It's not going to stop me, but man, that sucks if they are cracking down on that

Damn assholes.
Did you use Ebay printed postage? I wonder if they are using that as a trigger? Another PO close by?