The problem is not your FSX:SE registry key. The problem is your FSX registry key which is still there, but there's no FSX anymore and it's pointing to an empty folder.
When there's no FSX anymore, FSX:SE should instead use the FSX registry keys. The FSX:SE registry keys are ONLY used when you installed FSX:SE *together* with FSX.
When FSX:SE is installed alone, it uses the FSX registry instead and NO FSX:SE registry keys.
So, if you don't have FSX anymore, the FSX:SE registry shouldn't exists and the FSX registry should point to the FSX:SE folder. This is what a normal FSX:SE installation should look like. You have wrong registry keys, because you installed FSX:SE and THEN removed FSX, leaving the FSX registry keys still there, but pointing to nothing.
As I've said, the correct situation with ONLY FSX:SE installed is to have the FSX:SE key REMOVED:
- HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator - Steam Edition\10.0
And the FSX registry key:
- HKEY_CURRENT_USER\Software\Microsoft\Microsoft Games\Flight Simulator\10.0
Pointing to the FSX:SE installation folder. This is a CORRECT registry for an FSX:SE installed with no FSX.