I have been working on a project in InDesign CS6 for months and most of these pages are that old. However yesterday this appeared every time I printed (I have printed this thing a million time before without issue). I don't recollect doing anything to change these pages to evoke the change. Every page with this set up has a box in the same exact spot other pages are fine. No idea what to do or what I would have done to cause this. This is my first post so any info you may need let me know!
Have you searched that area on the master page to see if a stray frame is built there?
Just checked and they are clean. Thanks for the tip though. They are fine on screen but print with that rectangle. It's strange
Do you have any layer's visibility turned off that might be hiding the frame object?