Fletch:
Thanks for the kind works, and glad you are finding MathJax useful.
The font-size is based on the em and ex sizes that you have specified (or their defaults if you don't set them yourself). Since MathJax in node doesn't have a browser DOM to with, it uses a very simple DOM that doesn't actually know the size of the fonts in your page, like a real browser does, so you have to specify the size my hand. MathJax will then set the font-size so that the ex height of its fonts match the ex-height that you give it (for the page as a whole). The formula is ex / mathjax_ex / em (where mathjax_ex is the ex-height off the MathJax font, which is .442) to get the scaling factor for the math (and multiplied by 100 to get the percentage font-size). Since the defaults for ex and em are 8 and 16 pixel each, the result is 1.13122127, or 113.1% (to one decimal place). Making the em-size 18 would get you 100.1%.
If you want to prevent MathJax from setting the font-size, you could set the matchFontHeight property to false for the CommonHTML output (rather than setting the scale factor or the em size). But setting the em and ex sizes to accurately reflect the base font for your page might be the better choice.
Davide