Header seating..

Yeah, I was going to say get some Remflex gaskets. I'm not suggesting this in lieu of fixing whatever the actual problem if possible, but the Remflex's are extra thick (like maybe about an 1/8" or so, from memory), soft, and will comform to a little shape or bumps. There's a couple other brands that are similar, but I've only seen/used the Remflex. They are a little pricey, but if it solves the problem, or makes a good seal whether there's a problem or not, worth their weight in gold.