Can you give us more information about your document and how you're using bookmarks? Are you using the bookmarks to navigate within InDesign, or are you creating bookmarks in a PDF you've created from InDesign, and navigating in the PDF?
Are there different sizes and orientations of pagers in the document? How are you creating your bookmarks? Are you selecting something when you choose New Bookmark? I can't replicate your problem.
Also: Please tell us what operating system (exactly) you're running. Please tell us (exactly) what InDesign version you're using.