By any chance, are you using MegaSceneryEarth Coverage for the state of Massachusetts, or at least the Boston area? The reason I ask is because if you do, photo real scenery tiles could cause problems with other airport or scenery files. I have similar problem at New York LaGuardia, and part of JFK. I'm using MegaScenery Earth for the entire NYC area, and it's causing aircrafts to sink in one area, while scenery bleeding through in other areas. In FS9 you can resolve the issue by making sure all sceneries are above MegaScenery, but in FSX, no such luck, not even with their multi fix.
Just a though, in case you were using photo real sceneries.