Do we have that on the wiki yet, Angel? If not, we need to add it. Since MathJax actually rewrites the entire page after loading, you have to make sure your Jmol applet is added within a script that runs only after MathJax is complete. Not sure if MathJax has a callback on that, but there is a div on the page that is hidden and is reporting MathJax progress.
Here is a rendition of that prior message on this list, updated a bit for newer JSmol.min.js versions.
It's a pretty simple solution. Really what the problem is is that both Jmol and MathJax are competing for the AJAX processing. For compatibility with MathJax, make sure:
1) you are using dynamic loading of the applet -- no <script> tags that use Jmol.getApplet() within the body -- use $(document).ready() to create all applets
2) then set the jQuery document ready event to monitor MathJax loading and only start in on the AJAX until that is done. For example:
This is not really a bug, I am just looking for an idiots guide to running both JSmol (jmol-13.2.8) in conjunction with MathJax (release branch v2.2) on a MediaWiki (1.21.2) site without getting a red [Math Processing Error].