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I have a Satellite Pro A300 with Windows Vista Business and some of my FN stop working.
I've already tried to re-install Value Added Package but it changed nothing.
Not quite sure why some of your FN buttons stopped working but the point is that Flash Card Support Utility controls the FN buttons and you should try to restart the Flash Cards firstly.
Go to ALL Programs -> Toshiba -> Flash Cards and restart this tool.
Furthermore go to Control Panel - Performance Information and Tools - Adjust visual effects
Here the option "Use visual styles on windows and buttons" function on the bottom should be enabled to let the Flashcards software work