There is a patch over at Interplay's site that fixes some of the problems associated with W2k. Are you sure that problem is occurring due to SK? Maybe it's just W2k, since W2k is not officially supported by ToB???
Here's the link for the patch if you're interested:
http://www.bioware.com/bg2tob/bg2tobpatch.shtml
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Now where did I leave that doughnut?!