Are you using the uninstall feature in control panel on your computer to delete FSX. It should be listed as Microsoft Flight Simulator. If you have the FSX disks, you can use them to uninstall FSX.
If you're familiar with using DOS commands to delete FSX, you can try that also. Or as a last resort you can take your computer to a computer repair shop and have them remove FSX, but they will want to charge you an arm and a leg for doing it.
Or, you can install FSX SE as a separate program on your C drive and it will work, they use totally different registry entries.. Just remember to use the Steam icon on your desktop to open FSX SE.
Good luck.