This has been explained many times already on the forum, the FSX engine doesn't really support sloped runways, the airport must be flat, so it's designed to be flattened at the official published airport.
This means, the higher your Mesh settings, the more you'll see a difference in elevation when the flattened airport will meet the terrain that in real world would result in a sloping runway.
Either lower your Mesh resolution a bit, until the effects is less noticeable, or live with it.