FIRST!!!!!! MAKE A COPY OF THE AIRPORT YOU ARE HAVING ISSUES WITH.
1. Open WED.
2. Select "Choose X-Plane Folder button to point WED to your X-Plane folder.
3. Find the Airport you are having issues with. (eg. Runways not flat, Buildings sticking up in the air).
4. When the airport loads in WED (if you do not see the window list on the right hand side of WED, go to the WED menu - View and select Restore Frames.
5. The first listing under the heading "World" is the airports "dat" file. click on this and at the bottom of the listings you will see various menus.
6. Click on "Selection" and then click on Always Flatten. (change the x to a tick).
7. Save the file and then Export Scenery Pack
That's it.
If you have trouble. let me know the Airport/s and if I have them I can help.
You can contact me at xplaneaddicted@gmail.
Regards.
Kev.