It depends how much they are "sunk". A few centimeters it's normal, and it's the result of the scenery being made in multi-layered native FSX polygons and, due to the fact it must be compatible with FSX and P3D, they must be raised a bit in order not to flicker over the terrrain.
The "real" fix, would be doing a native P3D version, like we are doing with KORD. KFJK will likely be the next one.