When I merge two PDFs created by Word 2007 the bookmarks in the second and subsequent documents link to pages in the first document instead of their corresponding document.
I am using the Word 2007 XPS/PDF plugin with standard size and ISO 19005-1 PDF/A compliance. The bookmarks are created from the headings.
When I use PDFs created by OpenOffice.org, the bookmarks are fine.
This could be a Word bug or Multivalent may not fully understand the Word 2007 version of PDF.