When I submit a paper to EDAS system for a IEEE conference, I met the problem: "The PDF file cannot be accepted: IEEE does not allow bookmarks in PDF files".
I use TeXworks (pdfLateX) to generate the .pdf file. In fact, I have checked my .pdf file, it does not contain any bookmark, also, I've added the sentences:
\usepackage[bookmarks=false]{hyperref} \PassOptionsToPackage{bookmarks=false}{hyperref}
to avoid the problem. Unfortunately, it still doesn't work.
Heiko Oberdiek (hyperref's author) said that there should not be any bookmarks in the PDF if the bookmark=false option really is being used and to check the .log file to ensure this is so.
He can help further once the question is moved to tex.stackexchange.com
Also, try compiling the bare_conf.tex starter file with
\usepackage[bookmarks=false]{hyperref}
and see if the problem also happens with that simple test pdf.