A single PDF looks exactly as expected on the DVD on which it was distributed. When the PDF was copied from the DVD to an Intranet location, extraneous bookmarks show up.
We created PDFs using Acrobat Pro 9. The original source files were Word 2007. We were extremely careful to only use Header 1 in the original source files, and also careful when creating the PDFs w/bookmarks. We did extensive testing on the PDFs (mostly to verify structure and content), on multiple platforms with different browsers, releases of Adobe reader, and versions of Microsoft and Mac.
The final PDF documents were distributed via DVD. When viewing the PDFs from the DVD, all bookmarks look exactly as planned and expected. When the PDFs were copied to an Intranet site, one of the PDFs now shows extraneous bookmarks. We have examined the original source file (MSWord 2007) but did not see anything in the text (Times New Roman -- 12) that woulds indicate why Adobe might have thought it should be bookmarked.