I was having the same problems many did, regarding scenery being installed, activated, but not showing inside FS9.
After 4 hours of testing and experiences, found the "cat out of the box"!!!!!!!!!!!!
I noticed some problem on the installer, because was giving me an error in the beginning, about something not be an integer, but not specifying what exactly. Since it didn't add the entries on scenery.cfg, I guessed it was related.
So, went to the file and "debugged" from top to bottom. Noticed several small errors, like having an entry with Area.000 and other Area.xxx and so on. So after 2 hours, I decided to renumber every entry from top to end. Manually!!! More than 400!
In the end of that boring work, guess what!!! DIDN'T WORKED YET!!!!!!!!!!
But the installer already worked nicely from the beginning. Tried everything regarding bglman and "associated" but no good.
And finally, I went to scenery.cfg again, and disable ALL scenery entries! ALL! Except the default and Zurich.
Guess what!!! Still...................NOT WORKING!!!
So on my final attempt, and getting back to my programmer background, I thought something could be still related to the numbers on the entries of scenery.cfg!
And when I renumbered manually, and because there were several entries with numbers like 3192 or 4123, I renumbered al with the format XXXX like 0001, 0002 and so on.
In a final attempt I took the leading zero off, because I "only" and until 0401, so still 600 entries available for the future, and.................
VOILÁ!!!!!!!!!! Scenery up and running!!!!!
And beautiful by the way!!!
Now I don't know what the developer did so that this happens at running time, but at least, I had the solution for me!
Wanted to share, maybe can help others.