Take a straight edge to the new cover. And also check the depth of the "pockets" for the cam and crank. It's possible that the cover is hanging up due to not being machined deep enough and the cam or crank is holding it up. But more likely I'd say you may find the new cover isn't flat.
You didn't say what gasket you used. There is a stock thickness and GPS sells a thinner one, 20 thous. But either way the cover should lay flat to the case, even without a gasket.