I often do a repair of FSX and Acceleration. I put the FSX Disc 1 in the drive and select repair when given the option. After that is finished, I put the Acceleration disc in and select repair when given the option. This usually (1) fixes FSX (to RTM), then (2) Acceleration runs SP1 and repair FSX to SP1, and then repairs itself.

If you want, you can get SP1 for FSX from here: http://www.microsoft.com/Products/Games/FSInsider/downloads/Pages/FlightSimulatorXServicePack1.aspx
and SP2 for FSX from here: http://www.microsoft.com/Products/Games/FSInsider/downloads/Pages/FlightSimulatorXServicePack2.aspx

Hope this helps