Firearms laws are state-based, and Customs is a Federal Body, that's why they can still confiscate the toy. But once they've done that they'll contact you, in which case you reply to them and let them know that either:
a) You live in a state where the toy is not outlawed or prohibited; or
b) You live in a state where the toy is prohibited, but you have a current valid permit/licence to own it and provide evidence
You will then need to go and pick up the toy from Customs.

Yes, it's a hassle, but it sure beats not having a permit which gives you NO legal grounds to claim the toy and Customs will incinerate it. I have heard of cases where people who had no permit had their toys seized and destroyed, but I've never heard of a case where someone had the legal right to possess the toy still be denied its return. Worst case I've heard would be like yoshi594's where you end up waiting ages to get the toy back, but at least you get the toy in the end (though I can easily imagine that the wait would be excruciating). <knock.on.wood>