If one is in a lake, that means it's not compatible with Ultimate Terrain.
Among other things, UT corrects the locations of bodies of water and shorelines. Apparently the airport was made in a stock FS9 installation and placed in a location that was dry, but that location is supposed to be water, so UT makes it water, leaving your airport afloat. You could relocate the runways taxiways and ramps with AFCAD, but any buildings and such things wouldn't move. It seems that the airport just isn't compatible with UT.
I suppose the height issue of the other airport is something similar, though I don't understand the exact mechanics of it. UT's mesh corrects the ground elevations, so apparently the stock FS9 scenery was lower than it should be at that location and UT raised the level of the ground. The part I'm not sure of is exactly why the airport is left in a hole, but I have a suspicion. Taxiways (and maybe ramps, I'm not sure) determine the level of the terrain they sit on; I've used them to contour terrain to make things like dams. Try changing the level of the airport with AFCAD, which should adjust the altitude of the taxiways and ramps along with everything else. That might work.
If it leaves your taxiways in trenches and everything else where it is, try making a big, wide taxiway that fits under the entire airport. Make the surface "unknown" ans see what happens. You might be able to do the same thing with a ramp; that would offer the option to Not "draw surface" (I think that's the wording; anyway, it's a check box in the properties window, and you'll recognize it.) That should make your new ramp invisible, but I don't know if ramps level the terrain like taxiways do. Might be worth trying...