Jezz, Do you have lots of "old" flight plans, saved flights, etc., in <C:\Documents and Settings\your folder\My Documents\Flight Simulator X Files>, or wherever these files sit in your 'puter? Are some associated with aircraft that have been un-installed? If so, you need to clean those out. Also, if you "log" your flights with something other than the FSX internal <Logbook.BIN> - same folder - back it up first then delete it. FSX will generate a new one on the next start.
The usual maintenance tasks, e.g., registry cleaning, de-fragging the drives, cleaning out all the "temp" files and interweb caches, etc., will also help.