What steps will reproduce the problem?

1. use custom html template with $if(math)$ $math$ $endif$

2. add options below to Mathjax.js extensions: ["mml2jax.js"], jax: ["input/MathML", "output/HTML-CSS"]

3. run pandoc with --mathml option

What is the expected output? What do you see instead?

Expected output is clean mathematical equations. But mathematics displayed via mathml and mathjax does not look good compared to what is rendered via jsmath option.

What version of the product are you using? On what operating system? pandoc 1.5.1.1. Ubuntu 10.04

Please provide any additional information below.

Support for mathjax added in 9cf27c92c136cce4785744542eaf962c05f1052c. There is now a --mathjax=URL option. Please try this if you are able to compile the latest version of pandoc from source.