What I do know is as Peter wrote, that is, if there is transparency from an effect or an image on one page and not on another, your print or PDF will be affected (except to hi-res printing).
So try adding transparency to an object on the master page(s) up in a corner. Then review/print a few pages that span pages with and without the issue and see if that resolves your issue. This method is far faster than changing the images themselves.
Mike