I have the same problem and have suffered from it since I first installed FS9. The problem usually occurs after I have added a new scenery or aircraft, but not always. Deleting the new add on does not cure the problem. I would love to know why it happens and a permanent cure.
To get FS9 to start, I remove the Terrain.cfg from the main FS9 folder (I have a copy of it on my desktop), just drag it out and drop it onto the desktop. Then start FS9, you will get an error message telling you that the Terrain.cfg is missing, but FS will load but some function will not display (the terrain is just a bit flatter than usual). Some times this is enough to cure the problem, but not always. I create a new default flight with different airport and different aircraft, load the flight and shut FS down and restart.
If that doesn't work, delete the Terrain.cfg then copy another one from the FS2004 CD1 (it is in one of the cab directories, but forget which one).
I don't know why it works or what the problem is, but it does work. It is bit bit like a dose of piles (a right pain in the ar5e), but it only take a minute or two....until the next time.