Yes, the change from the old 600 metre default mesh in FS2004 to the new 75metre mesh in FSX means that most airports have new elevations. Just using the FS2004 AFCAD will glue the airport facilities to the old elevation, which causes the plateaus or holes.
There's also (usually) a flatten polygon under the airport, to match the facilities elevation. So to fix this, you need to:
1. Delete the old flatten;
2. Create a new flatten;
3. Change the AFCAD elevation;
4. and sometimes you need to put a copy of the AFCAD file somewhere where it has a much higher priority -- I used Scenery\World\scenery.
To do the first two, I use FSX-KML, available from the
FSDeveloper.com site.There's plenty of info on how to use this on the FSX-KML site, but it's relatively easy -- you just need Google Earth installed. You draw your flatten polygons in Google Earth, save them, load them into FSX-KML, tag them with a flatten tag, and generate a flatten (or exclude-flatten) BGL.