I have used master pages all the time and have have never had a problem with it in CS5. I now am on a subscription for creative cloud and started having this error in CS6 and it has continued into CC. When I add a new page or change the position of a page in my document, the master page moves out of position and covers 1/3 of the page. I have found some help online, the new page tool let me slide the master page back into place. However when I next add/move a page it messes up the master page on all of the following pages for the rest of the document. I am unsure if this is an issue with my settings for page shuffling (I tried to keep it the same on all my pages and masters) spread shuffling or the page tool. I hope this is enough info to get help from. It is hard to describe well.