So I assume that you already tried the Disk Utility "repair permissions"?
Otherwise I don't really know why this is causing you problems. I remember I used to have a problem with audio codecs on my iMac, which caused all sorts of problems. I fixed it by starting and quitting GarageBand; don't know if that will help you any.
Short of that, the only thing I can think of is a reformat, which although drastic would almost certainly solve the problems you experience.
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