Well guys;
I found what was causing this issue on my system. Turns out there was a file called...
KDCA_Reagan_National_dca2002_4pt880.bgl
located in my FS9/scenery/name/scenery folder. Once I removed it two problems were fixed. Once was the runway elevation problem where the runways were a foot or so lower than the rest of the field. And, a problem where much of the ground textures would not load if KDCA was my destination. So I would be taxiing in over grass.
I don't know the origin of this file. I suspect it might be from Shez Ansari's KDCA 2002 scenery which I had installed at some point prior to acquiring the Cloud9 KDCA. But, I recently re-downloaded Shez's KDCA2002 and no such file exists in the package so I'm not sure.
But if your having the same issues in FS9, look for that file and remove or rename it to disable it. Fixed the issues for me.
Dave