OK sorry for the delay Tony do you have Teamspeak or other Voice client that you use and we can communicate with and I can walk you through as this may I think be far quicker than folloeing a big post line for line.
I frequent a TS server here where we ONline fly at an IP of 61.9.196.112 Called Australian VB NAv Challenge
On your desktop you'll have an icon pointing to "My Documents" Now mine isn't where Windows expects it to be , I don't have nothing on my "C:\" except the OS nothing - except maybe some software that does not allow me to place it else where of NEEDS to on "C:\" to run correctly.
Now I had some files in a Flight Simulator Files directory that for what ever reason appeared there in the corse of play.
This started to confuse the FS Kernal and it began to argue and essentially stop responding due to not being able to distinguish which file and or directory to use.
Anyway I deleted all in that directory after first zipping the contents as a backup precaution.
Then I followed this course of action.
START - RUN - EXPLORER ( I hate the My Computer) ((No Tree)) Now Select TOOLS and then Folder Options - Then Select VIEW from the Tabbed menu and then you should see the settings on the left, you need change your settings temporarily to those on the right
This is so you can navigate to here and actually see the directories below.
Like this " C:\Documents and Settings\Maurice A.C. King\Application Data\Microsoft\FS9"
The main files of interest are highlighted, save these as a Zip and then delete them.

Note the highlighted Directories.

I had a copy of those above somehow attached to my Flight Simulator Files Dir that resides ( on my system at least ) on "D:\" ie "D:\My Documents\Flight Simulator Files"
I pruned this down to leave just the Directory below

After all of this then I reset the Hidden Directory, Why? Windows doesn't have to search for it, being hidden it's indexed and therefor Windows and more importantly FS9 knows where to find things with out arguments with the OS. Another trick is actual set your user profile so once again Windows and FS9 don't have to go looking, all of which drags time and processor power from more important tasks like getting FS running.
Maurie I hope this helps
Worst case edit the registry and delete the referance to FS9 and install over the top restoring corrupt files, back up your Aircraft and scenery first as a precaution.