I think all I need to do was print to a pdf and not export to a pdf.
Just the same any additional comments for the future would be appreciated.
Never print any PDF from InDesign, Illustrator or Photoshop. Export them. Printing PDFs is soooo last millennium, Yesteryear technology.
Be sure you have unchecked spreads in the dialog box.
Since you are using CS5.5 I'm not sure you have the spreads/pages option in the export PDF (interactive) dialog, which is the default PDF export. When you export, use the Type dropdown to choose PDF (Print) and you should be OK. Spreads is off by default in Print-flavor PDFs.