When you install TotSC, the installation program asks you whether you want to modify the saved games so that you can use them with TotSC. If you havent done that, you can do it now by running "MConvert.exe". This file should be in your BG directory, it will update your savegames and you will be able to use them with TotSC.
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"Let my spells do the dirty work" Ertai, High Sorceror of the Holy Flame