If you have two different typefaces in your document then you are going to have variation in line heights. You might also have variation if you apply superscript or subscript to something (eg have a footnote). Are ALL styles specified with the exact same line height and zero space above and below?

If EVERY line on EVERY page was EXACTLY the same height, there SHOULDN'T be variation but maybe there is another factor in play that we haven't yet worked out. Some versions of Word document formats treat spaces at the top of the page differently - perhaps you could try looking at the Compatibility Mode of your Word 2013 document or also look at the document layout options at the bottom of the Options > Advanced area.

In terms of the margin settings, lets say your useable column height is the page height minus the top and bottom margins. Now lets assume that your content, for whatever reason fits either x or x+1 lines of content on it. Perhaps the variability is due to a margin less than one line - say 259mm of height fits 30 lines but every now and then it fits 31. If you varied the bottom margin by 1mm, you might discover that every page now contains 30 or 31 lines exactly. What about changing by 2mm? There may be a sweetspot where you get consistency on the line count.

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Andrew Lockton
Chrysalis Design, Melbourne Australia