have you also removed thru add or remove programs all of the add ons such as captainsim aircraft etc? maybe these are interfering even thought the installs are gone at least we could see if they are still in add or remove programs in the control panel also remove all other addons aircraft, weather, scenery, online atc, etc remove anything involved with flight sim after making sure you have everything backed up, then do a complete uninstall of fs9 and reinstall start it, then if it works install the patch.
I am not an expert just trying different options. I hope we can get it fixed for you.