Hi TJ,
In Powerpoint, you should have both an Acrobat and a Preferences option in the Acrobat ribbon. The Preferences button opens a dialog where you can check a box for convert speaker notes to text notes in Adobe PDF. There is no option for this in Acrobat, you'll need to do it from PPT.
Hope this helps,
Dimitri
WindJack Solutions
www.pdfscripting.com