- How is your footer done? Do you use Object Style and Paragraph Styles for text. This is a must.
- Do the footer get the Information from a text variable? This is recommended.
- Do you align to baseline grid? It would help to align text vertically.
In addition to what Willi said, make sure that the same master page is applied to all of the document pages for consistency. Also, is there any chance that the page size changes on some of the pages? Sometimes users will accidentally change this using the page tool and this could cause the problem that you are seeing. There's definitely something strange going on. I use this all the time.
One more thought... if all of the body pages are based on the same master page (or on duplicate master pages that are based on the parent master), then the only way this can happen is by overriding master page items.
Reapply master items
If you’ve overridden master items, you can restore them to match the master page. When you do this, the object’s attributes revert to their state on the corresponding master, and will once again update when you edit the master. The local copy of the object is removed, and the master item cannot be selected, as indicated by its dotted border. You can remove overrides for selected objects or all objects on a spread, but not across an entire document at once.
- Do one of the following:
- To remove master overrides from one or more objects, select objects that were originally master items. In the Pages panel, target a spread and choose Remove Selected Local Overrides in the Pages panel menu.
- To remove all master overrides from a spread, in the Pages panel, target the spread (or master spread) from which you want to remove all master overrides. Choose Edit >Deselect All to make sure that no objects are selected. In the Pages panel, choose Remove All Local Overrides in the Pages panel menu.
If you’ve detached master page objects, you cannot restore them to the master page; however, you can delete the detached objects and reapply the master to the page.
If you reapply a master to a page that contains overridden master page objects, the objects with overrides are detached and all master page objects reapplied. This may result in two copies of some objects on the page. You’ll need to delete the detached objects to exactly match the look of the master.