Are you sure that the (partial) mess up is gone, so did you check that the FSX main folder got deleted, the all user profile and your own user profile of FSX got removed?
How long did you wait. The first FSX startup can take up to 10 minutes on a system with bad fragmentation or a slow disk, FSX not resonding in this time since it builds up.
Another idea might be that your system has problems to go to the Full Screen mode, or wants to issue a message that displays behind the full screen ( in this case you do not see the message and the system waits for you to click OK
to a message that might be easy to fix. Since FSX runs full screen with effectively half resolution of windowed only anyways, try to start in windowed mode...
If this does not help, ask the question with some more details on a dedicated FSX forlum like the one at flightsim.com.