Hi Lorin,
It's tough to analyze this without digging into the stylesheet itself, but it seems like the first and third entries are using the same element (toc), so if toc is checked for bookmarks, both will be included. It may also depend on how your elements are defined in the DCF:
http://support.ptc.com/cs/help/arbortext_hc/ae61_hc/index.jspx?id=help7729&action=show