I had cs4 and my book of documents could export my 60 page book just fine.
However, when I converted everything to CS6, the start page for the PDF is now on the left, even though in InDesign it shows on the right. This throws off the printing big time.
I've already checked and the documents are "facing pages" ... not really sure how to correct this as I never had a problem in cs4. Thanks.
Check your view settings in Acrobat. I bet you have it set for facing pagres, but neglected to tell it there was a cover page.