Might be a stupid question, but are you cross tightening the head bolts? I usually snug all bolts just so they are touching the head, then set my tourque wrench in inrements, and work my way up to the spec. Always tightening in a criss cross pattern. ie, set my wrench to say 9ft/lbs, and tighten all bolts to 9. Then set it to 12, and tighten them all to 12, etc. might be overkill, but might as well spend a little more time doing it just for extra insurnace. Im at loss for any other ideas, other then having it milled again, but this time just skim it, maybe take off .002-.003" only.