Problem on Using Mathjax with Jekyll Markdown

[ByzanTine]

Hello,
I am not sure if it's my mistakes, but after I tried a lot, I still get weird result with a jekyll theme using Mathjax.
I tried to write my blog
http://byzantine.github.io/ByzanTineBlog/%5B%22machine%20learning%22%5D/hmm-and-viterbi/
And the first three latex expression use three different method. You may find the .md here
https://github.com/ByzanTine/ByzanTineBlog/blob/gh-pages/_posts/2014-05-28-hmm-and-viterbi.md

The problem is when I am using $$ $$, it display as inline. And when I am using [ ... ], it works pretty good but when I do a little bit complex expression like

[P(z_t|z_{t-1} z_{t-2}) = P(z_2|z_1)\quad t\in 2...T]

Then it won't render properly.
In case you can't see my page, here is the .md file

And here is the output

By the way, here is the config of Mathjax I am using

Hope somebody can help me out!

[pkra]

This is a common problem with Markdown and MathJax interacting badly. The problem is that the markdown processor runs first and transforms _...._ into <em> ... </em>. This alone would break the rendering; in addition the TeX preprocessor will stop at HTML elements, so the \[ and \] are being ignored.

For more information, see http://docs.mathjax.org/en/latest/tex.html#tex-and-latex-in-html-documents.

[pkra]

I almost forgot: to fix this, just use markdown's escape mechanism and turn _ into \_ . That way, Markdown will convert \_ to _ in the HTML and MathJax will be happy.