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Thanks for the report. This is due to a problem with the way the eqnarray environment (and similar ones) try to arrange for the spacing at the beginning of the second and later columns interacting badly with the implementation of \mathchoice that is used by \choose and similar macros.
This is fixed in the issue1053 branch of my fork of MathJax.
When I insert a binomial coefficient in an equation array like this:
\begin{eqnarray} C & = & {n \choose k} \ \end{eqnarray}
The first parenthesis is rendered smaller than the second.
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