The valve covers should sit flush all the way around. Them being warped is unlikely. Something is likely catching or not installed right. run your finger around the gasket mating surface and make sure the gasket is seated all the way around. Did you remove the guide tabs? my first thought (if you didn't) is that the rear tab is catching and not allowing the VC to fall into place all the way. If you removed all the tabs I would take a look at the VC from as many different angles as possible to figure out where it is catching. take it back off if you have to and look at everything. Take your time. You don't want to break anything costly, or even cheap for that matter.

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2007 E70 X5 4.8i Sport Package
8x,xxx Miles
"My Precious" (Smeagol voice)