Well, I called up Sony support and they have been of no help. The support person, I could tell from they way she as responding to my question, didn't have a clue what I'm talking about.
So, does anyone have a solution? I don't know why the bookmarks that were created on the PDF file are not showing up at all. The PRS-700 CD comes with a PDF manual. The PDF manual also has bookmarks and those bookmarks on the Sony show up as a "Table of Contents". I can click on the "Option" key in the Sony and a "Table of Contents" will appear.
However, PDF files where I added the bookmarks are not showing up as "Table of Contents" on the Sony. They aren't showing up at all.
I'm using Acrobat Pro 9 for Mac. I also have access to Acrobat Pro 8 for Macs.