Dave
What version of Acrobat and PowerPoint are you using? What method of conversion are you using - PDFMaker or printing to PDF?
If you are printing to PDF then it could be that the page size in Office is different from your Acrobat distiller printer (or, in Acrobat 6 the Adobe PDf printer).
You can run a batch process to crop - or uncrop the pages which can take care of the ones that have already been converted, but more information on exactly what you are doing will hopefully bring about a more permanent solution.
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