That tells me your flange is out of shape. Like Greg H. said above and confused himself, the bolt holes have deformed the metal. So no matter how tight you screwed the bolts, the cover flange would not get any closer to the block's edge.
You could have straightened out the flange properly, or used a thicker gasket. I am glad it worked. If you have trouble again, examine the flange and bolt holes better. It should be flat.
