I would install "Autosave". So at least you know where the issue happens. Then you should backup your scenery.cfg and deactivated all sceneries and aircraft by renaming the folder temporarly. After having got an almost "virgin" FS9 you might restart at the last saved situation by Autosave. I would even install an additional basic FS9 and see what happens. Don't forget to backup FS9.cfg first. If basic FS9 is working correctly, than you could paste on sceneries and aircaft step by step and restart your FS9 every time at the said situation. It takes some time, I agree, but it could be a solution.