I noticed the same happening to my AFS4. I checked the tm.log and saw that after moving some custom scenarios to (what I believed) an archive directory, I actually led AFS4 on a wild goose chase for missing files.
Properly deleting the files restored my boot-up time for the simulator.
For a quick test you can rename the Aerofly folder in your user documents directory, essentially starting with a clean slate. If this fixes your problem, you know that your user directory is to blame, and can re-renane the directory to start checking for the main cause.
Thank you, thank you, thank you Armitage!
You were spot on - something corrupted in my Documents folder. Renamed my old one as you suggested, started up the program to create a new Aerofly FS4 folder and it loads in 5 seconds like it did before. Now copying over the subfolders one by one to keep my bindings/preferences, etc.
Thanks again...