I suspect that we would need a lot more information to help.
When you say "section" are you talking Word Section or logical section?
Take a look at your document in Draft view. Are there any section breaks on the page?
Does simply double-clicking in the footer modify the pagination? What do you mean when you say it does not correspond with the footer?

If possible, scrub a copy of your document of anything confidential or proprietary and post it as an attachment here or a link to an online location. You can add an attachment using the Go Advanced button and clicking on the paperclip icon.