I needed to re-use an existing pdf (for a business card, with bleeds and marks), which was last saved with AI CS6. So, in order to get the filename in the "new" pdf to reflect the new use, I opened in in Illustrator CS6, and just re-saved with the new filename. Now my 1-page pdf suddenly has 4 pages; pages 1 and 2 look like they should, but pages 3 and 4 don't have bleeds showing.! What???
I used a custom in-house joboptions file for the settings; this joboptions file did start in InDesign, but has never caused problems before, and I have used it often in Illustrator.
I just deleted the extra/new pages, and proceeded, but I am confounded by this.