Before I begin, I just want to say that before you make changes to your original files in FSX,
Make back-ups/copys of your orginals! If you install 3rd party scenery into your add-on scenery folder, and it messes things up you can always just go there and delete it, and things should get back to normal.
If you add scenery or aircraft that is going to change any original files in FSX, you have to open those files some place else (make a new folder), so you can see what your installing, so you can make copys of those files that will be changed.
Now not to insult any of your
Great Designers out there, that use autoinstallers;
If you download 3rdparty scenery,aircraft,and utilities that have an autoinstaller, I choose to use the autoinstaller to open in a folder that I want (again, cause
I, want to know what files/folders will be added or changed, so I can make copys.), not just to let it open in FSX, because orginal files could be changed, and you don't know which ones, and if it causes a problem,and you'll get stuck doing most likely a dreeded reinstall.
OK, as far as using the repair option, from what I've learned (by using it), is that the repair option works by trying to replace all files and folders back to there original state, and sometimes it works fine and sometimes it can make things worse,especially if you have added a lot of stuff, because it doesn't do a good job getting rid of files that might have got corrupted.
SO, before you try the repair option, try doing this:
Not to sound like a broken record,
make back-ups of these files before you do this fix.
Delete your FSX.cfg file.Fire up the sim and it will write a new one. Most of the time this will bring things back to normal, and the only thing you'll have to do is reset your settings (cause every thing gets reset back to the default).
Also your
Logbook.BIN might have got corrupted, and you'll have to delete it, and let the sim write another one. The thing that sucks about this fix is that you lose all your logbook entrys.

These 2 fixes have saved me alot of times to quickly fix fatal errors.
So, what you might have to do, is do the dreeded reinstall and start fresh. hope this helps you, and gets you back flying.