I'll answer in both places as I think people searching for the issue are more likely to land up here.
Thanks for reporting. It is a bug in CodeRunner, exactly as your github posting identifies. I have a tentative fix, but I want to see if it creates any new problems before releasing it.
In the meantime, here's a workaround (slightly ugly).
<span style="display: none;"></span>
- Wrap your LaTeX equation in the MathJax span you identified above: <span class="filter_mathjaxloader_equation">...</span>
Alternatively, if you want to live on the bleeding edge, you could checkout the development branch on github. Probably you'd only want the latest commit (to renderer.php) addressing this bug as some of the other changes are work-in-progress.