Jere,
In addition to Arnis' tip, I have noticed that if I add pages to a document that does not use the default left/right master pages, then the newly added pages are formatted with the default left/right master pages. So, I have to reapply the master pages to the left and right pages for all the pages in the document. Typically this happens for files such as TOCs and Indexes, in which I have set the custom master pages early in the cycle and the files grow as the book gets bigger.
Van