Hi Nigel -- and thanks to Tom for the mention. Yep, I'm here, but I've been on vacation (or holiday, depending on where you live) for 12 days and have only returned to the office today.
I wasn't able to view your screen shots (nothing happened when I clicked the link), but I believe I understand the issue. The issue isn't a bug in either iBA nor MathType; it's expected behavior. As you know, you can indeed change the fonts in MathType to your liking -- or at least mostly so. In iBA, you can do so with text as well, but not with equations. (You can change the font color of an equation by changing the surrounding text, but not the font face.) You've already discovered iBA uses MathML to represent and render equations. This is true no matter which of the 3 methods of inserting equations you're using (MathML, LaTeX, or MathType). There's a different means of setting font in MathML, but iBA doesn't make it easy to do so. These are things that only Apple can change. If you're so inclined, here's a feedback link to let them know how this impacts you: http://www.apple.com/feedback/ibooks-author.html.
We have an article about using MathType with iBA, but it doesn't address fonts. I need to correct that. Meanwhile, here's the article: http://www.dessci.com/en/support/MathType/works_with.asp#!target=ibooks_author_m ac.
Bob Mathews
Design Science
