The MathJax version pulled down with the webwork svn is MathJax 2.0. You can be sure that you are running 2.0 by loading a page which displays math using MathJax and then right-clicking on the math and selecting "About MathJax." Or, on the server you can do the same with the test files in webwork2/htdocs/mathjax/test/.

Also, here's a post about the IE issue from the mathjax team:

http://www.mathjax.org/2010/08/25/news/mathml-in-html5-problems-with-ie9/

Thanks,

Jason