In the "old "days a check ball seat for a accelerator pump could be restored by "swaging" the old ball into it before replacing the ball, this smashed the seat surface to give a good seal, however, the ball in a holly secondary diaprham is not a check ball, it is there to slow and regulate the opening rate, there should be a tiny groove cut into the ball seat. If this groove is gone you must etch one into the seat. A metal scribe works well, don't worry about making it too big, but make sure it allows air flow, like you described, also helpful is a small amount of lube around the screw holes to keep the screws from wadding up the rubber diaphram. Of course you made sure the hole in the diaprham was indexed properly, so that is not oyur problem.
Just trying to be of assistance, not rude. Good luck, Scott W.