There must be something in the formatting of our documents that's different then. For me adding a paragraph (or indent) before the page number pushes the text up.

I've been able to find a workaround here (using the ruler to push down the page number once the footer is active). The problem is I have to do this in every section (my document has many), while changing the margin works across the document, so it's not an ideal solution (still interested in a better one...).

To clarify: from what I understand, the size (height) of the margin and the one of the footer seem to be independently set; and if the footer laps over the margin (if the footer is larger than the margin), the text will stop where the footer begins, not where the margin begins (maybe this is also true the other way round, i.e. if it is the margin that's larger, haven't tried; but I would guess so). Depending on whether that's the case, Charles Kenyon's solution may work or not. (If adding space above the page number makes the footer lap over the margin -- or if it already laps over the margin to begin with--, it pushes the text up; if it doesn't it doesn't). I may be totally wrong here, but this is what appears to me to be the case.