Those results are a product of the differences in line spacing (which varies between multiples of 1.15 and 1.25) in your document. I note, too, that you're using empty paragraphs to generate the inter-paragraph spacing instead of using paragraph before/after spacing. Hence, the inter-paragraph spacing also varies, according to whether the empty paragraph has a line spacing of 1.15 or 1.25. To fix that problem you'll need to adjust the line spacings so that, regardless of the font used, it is always the same. Even so, you're liable to end up with a different space if a paragraph ends at a page boundary - which, with your present approach, might even result in an empty paragraph at the top of a page.

One might also query why some footnote references are bolded but other are not...

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Cheers,
Paul Edstein
[Fmr MS MVP - Word]