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lslbrian: As i run both Tie fighter and X-wing 1998 versions i get constant flickering of my desktop. the game runs great. I tried every compatibility setting and no luck. Any known way to fix this...its almost unplayable since it happens every 30 seconds.
Do you have anything running in the backround, like skype, antivirus app, anything that might try and steal the focus from the game? Try turning it off and running your system as cleanly as possible and see if it works.
Masoniter: Same problem here. Elements from windows flicker on the screen, like icons in the system tray or parts of the desktop.
Alt+tab out of the game, press ctrl+shift+escape and shut down the explorer.exe process and see if it helps.

After you are done with the game, press cmd+r and type "explorer.exe" and press enter to bring the explorer back.