Exactly what I heard. The early ones had problems with holes lining up. I purchased the valve covers 4 months ago from Summit. Fit like a glove. First thing I did to make sure I did not get an early set was just put the gasket on it. Gasket lined up perfect. So you may have gotten an early set. Where did you get them? Its possible you can return them. Even though you painted them, they would have not fit anyway. You may be able to contact AMD for exchange. Although last I heard they were on back order at the time I ordered them. Just happened that Summit had them in stock.

Or, is it because your heads are modified due to rockers being higher than stock? That is the other issue.