You might try creating the PDF from postscript rather than Frame:
1) Open the book and all files in it.
2) Print the book to a postscript file using the Adobe PDF printer option.
3) Double-click the postscript file to start Distiller and create the PDF.
>I'm using Frame 8.
>I have a book (28 chapters) with a TOC. I'm creating a PDF using the File >
>Save As PDF command...
>I can make a PDF of the TOC on its own. Works fine...
>If I put the TOC in the book, I get this message in the log file where the
>%%[ Error: undefined; OffendingCommand: pdfmark; ErrorInfo: Rect ]%%