Intake manifold won't seal - How do I check it ?

I did plastigage with the gaskets. The gaskets are Edelbrocks with the sealing bead around the ports. I put the plastigage just outside the bead. A section of the plastigage did run through the bead on one port and it smashed to nothing. The plastigage is .004" thick according to the chart that the plastigage comes in. Bolts are not too long and thread all the way up.