Every time that I see/hear the phrase "Microsoft Word is ignoring all of this" (or similar comment) the first thing that come to my mind is that you are doing something wrong. With your narrative description it also appears you have other problems (ref your bullets comment) other than page numbering. With that in mind, the below listed links may help you:

http://www.addbalance.com/usersguide/sections2007.htm
Working with Styles
Understanding Styles in Microsoft Word



Other posters may offer additional assistance. Hope this helps...

Well, clearly I am doing something wrong, thus the question and situation I am presenting. The phrase "Word is Ignoring" is because "Link to Previous" is unselected, yet, each footer is still linked to the previous footer, which is why I change one, and everything changes.

I'll sift through the links you provided. Thanks.

Somehow, I doubt you've actually unlinked the Section footers; your description suggests not. I've used Word for 25+years and have never encountered such behaviour, nor is it one I recall seeing documented elsewhere. I trust you're aware that unlinking Headers, for example, doesn't unlink footers and that each Section has three headers and footers - primary, first page and even, the linking of each of which is independent of the others.

__________________
Cheers,
Paul Edstein
[Fmr MS MVP - Word]