Mark,
I saw this interesting peace of text from years ago:
Maybe you are lucky to to solve your completing setup problem
Well, i reinstalled FSX once more, but after getting all Microsoft's updates and fixes etcetera (i had a hard time finding back this page with newly installed Explorer 7, somehow i lost all my old bookmarks). After installing FSX i found out that nothing had changed. Still "completing setup" every time i started FSX. Then i found a posting by someone about incompatible hardware. So i tried unplugged my joystich (it's a SpeedLink BlackHawk, el cheapo but it serves me fine with lots of convenient buttons, thrust handle and a twistaxis for rudder). After uncoupling the USB plug i restarted FSX and voila no more "completing setup". Somehow the joystick prevented FSX from finishing its setup. After plugging the joystick back in, FSX continued to work OK. No more "generating scenery indexes".
Regsrds
Berend