Hi Sam,
I would be a little surprised if MathJax had the wrong font. It could however have the wrong size. There is adjustment in the context menu for the user to change this. If all expressions are too large or to small compared to the text around them, this is the problem. To adjust it, right click an equation and select Math setting -> Scale all mathematics from the popup menu. Change the percentage to scale the height until it matches the line.
Daniel