I selected Export pdf when going through publishing. I tried to view the output but nothing displayed. I checked the publishing folder. All files are included except the pdf file. Why didn't the pdf export to the publishing folder?

That option in the publishing dialog is intended to create a PDF version of the same content you are publishing to SWF or HTML5.

Is that what you are trying to do?  Or do you have some other PDF that you were linking to from a slide on the content and you were thinking that checking that box in the Publishing dialog would ensure the PDF was exported with the content?