Q:

Does anybody use Pancake? MathJax

$$\begin{align*}a_1=\alpha _1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots a_1 \end{align*}$$

Delete a_1 in the above, then that could be shown well.
$$\begin{align*}a_1=\alpha _1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots \end{align*}$$

http://hypergroups.pancakeapps.com/Test/test.txt
Of course they can show well in Math.SE
$$\begin{align*}a_1=\alpha _1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots a_1 \end{align*}$$
$$\begin{align*}a_1=\alpha _1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots \end{align*}$$

The MathJax here and Pancake are not the same?

The latex codes aer in the post. You can create a .txt file and add the mathJax script codes which could be obtained by saving my webpage linked to get the ... codes, because I cannot put it here, Math.SE compile something about that.
---something wrong with the follwoing code, How can I keep a raw codes in Math.SE?
<script type="text/x-mathjax-config;executed=true">
MathJax.Hub.Config({
tex2jax: {
  inlineMath: [['$','$'], ['\\(','\\)']],
  processEscapes: true
  },
TeX: {
            equationNumbers: {
                autoNumber: ["AMS"],
                useLabelIds: true
            }
        },
        "HTML-CSS": {
            linebreaks: {
                automatic: true
            },
            scale: 85
        },
        SVG: {
            linebreaks: {
                automatic: true
            }
        }
});
</script><script type="text/javascript" src="./Pancake.io_files/MathJax.js">
</script>

A:

It looks like Pancake is using the underscore to initiate italics (notice how everything between the first and last underscore is in italics and the underscores have been removed).  Since the Pancake processing is done before the MathJax processing, this means that Pancake has modified the math to remove those underscores and insert <em>...</em> tags.  That will prevent MathJax from processing the mathematics, since it doesn't process anything containing HTML tags.
In order to get this to work, you would need to be able to tell Pancake not to process underscores inside the math delimiters.  The best solution would be to modify Pancake to know about MathJax delimiters and not modify anything inside.  But you may also be able to work around that by using some sort of "verbatim" mode (that allows you to provide unmodified text).  In Markdown, that is handled by a back-tick, so `$...$` would allow you to enter mathematics unmodified.  But this may cause the math to be enclosed in <code> tags, and you might need to modify the MathJax configuration to remove "code" from the skipTags parameter in the tex2jax section of the configuration.
PS, I see @robjohn has identified the <em> problem already.

A:

The relevant code from that page is
<p>$$\begin{align*}a_1=\alpha <em>1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots a</em>1 \end{align*}$$</p>`

<p>$$\begin{align*}a_1=\alpha _1+\alpha _2+\cdots+\alpha _n,a_2=\alpha _1\alpha _2+\alpha _1\alpha _3+\cdots+\alpha _{n-1}\alpha _n,\cdots \end{align*}$$</p>

My guess is that the <em>...</em> tags are preventing MathJax from processing the first paragraph.
It seems like a preprocessing step is changing the underscores in the latex source into italic text in the HTML.

