You need to get legal advice, and quickly. You haven't done anything wrong with the birth certificate, and he has. Get it sorted out, for God's sake!!
I can still remember my Health Visitor coming round to see my first son at a few days old and asking whether we'd registered his birth. I said that my hub had done it that morning, and her reply was "Oh that's right, you're a respectable married couple aren't you?" as a joke. Joking aside though, he had to take our marriage certificate in with him, and there is NO WAY he could have done it without.
Something is not quite right here, and I hope for all your sakes you get it straightened out as soon as possible xx