It sounds as if your best bet is to do a complete uninstall and reinstall of SoA/ToB. It sounds as if you are supposed to have some files somewhere that you don't.
That would be my recommendation, although you could also try over at the BlackIsle/Bioware forums.
http://www.blackisle.com
Sorry I couldn't be of more help!
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Now where did I leave that doughnut?!