On mechanical cam engines I typically use sealant on one side of the gasket only. Make sure the valve cover is totally clean and the flange is not bent, no warped bolt holes, etc... Then apply a heavy coat of Permatex gasket compound to bond the gasket to the cover. This way you can remove the cover several times without having to replace the gasket.
As for rubber vs. cork, I think the cork probably seals a bit better, but the rubber is less prone to shrink. Either way when they get old and hard they leak.