Every time I start FSX it gets stuck at the splash screen with a message saying "FSX Stuck on "Completing Setup: Generating Scenery File Indexes" at 72%.

Try to delete files inside SceneryIndexes-folder from C:\ProgramData\Microsoft\FSX and let FSX rebuild those indexes.

 

 EDIT i didn't see that you are using FSX-SE, so find equivalent files folder for FSX-SE and remove those scenery indexes.

Try to delete files inside SceneryIndexes-folder from C:\ProgramData\Microsoft\FSX and let FSX rebuild those indexes.

 

 EDIT i didn't see that you are using FSX-SE, so find equivalent files folder for FSX-SE and remove those scenery indexes.

Well that worked.

Great ☺