I am laying out a book in Adobe InDesign.
Context: Since creating the original book document, I have changed the page size from 6x9 to 7x10. All my master pages are of the new size (7x10). (I have a feeling this relates to the problem somehow.) I have page shuffling turned on.
When a page shuffles from left to right or right to left (due to an earlier chapter changing the number of pages), the master page moves -- and is now misaligned with the page.
After shuffle -- note how the master page no longer overlaps the real page correctly (which messes up a bunch of other things).
If I right click on the page and re-apply the master page, it's fixed. This is a pretty long document and I can't do that for all the pages. (I could one time -- but doing that every time a page changes is going to cause a lot of issue.)
Added some more screenshots with simpler master page, where nothing is off the page. The same thing happens.
Before shuffle. Note how the master page correctly sits immediately on top of the actual page, with the correct boundaries.
After shuffle. Note how the master page is now misaligned with the actual page.