I have the following segment of Markdown with embedded LaTeX equations:
# Fisher\'s linear discriminant
\\newcommand{\\cov}{\\mathrm{cov}}
\\newcommand{\\A}
In Word 2007, I see a result similar to yours, except that here, I don't see the "question marks in boxes" characters, just space.
If I then take one of the expressions, and use your trick of going to linear display and back, the characters reappear for that expression.
If I save and re-open, the other expressions still do not display correctly, but if I save and look at the XML, I notice that
Since Word 2010 displays the resuls correctly, I can only assume that it does not rely on these explicit font settings, whereas Word 2007 does. This doesn't really help you yet, because altering all those w:r elements would be even harder than what you are already doing. But it is possible that a default style/font needs to be set, either somewhere higher in the XML hierarchy, or perhaps elsewhere in the .zip (perhaps in fontTable.xml or styles.xml). I'm not familiar enough with Word's XML structures to guess what, if anything might be missing, but may be able to have a look tomorrow.
I suppose another possibility is that you just have to have all these extra rPr elements for this to work in Word 2007, which would suggest that pandoc may have been written for Word 2010, not 2007. (I don't know anything about the tool).
As an example, where you have
(
what you need is
(