Sometimes a header flange can be slightly warped, but the only way to tell is to removed it and test it with a machinist straight edge. My BBK's would loosen over time, this was before locking header bolts. I'd try some of those Stage 8 locking bolts or there are some that have a set screw in the middle that when tightened spreads the outside bolt. Try the cheapest first...could be a gasket too, if the manifold was left loose and the exhaust has been allowed to burn the gasket.
Hope this helps.