Have not investigated this in any detail, but have also noticed a clash between JSmol and MathJax in some circumstances - with MathJax displaying a [Math Processing Error].
In case it helps with the diagnosis, here are the symptoms I have observed. Behaviour is somewhat variable. Firefox appears least susceptible, Chrome and IE more so. Sometimes a page reload fixes the issue, sometimes it breaks a working display. The problem appears worse for pages with more, or more complex, JSmol instances. So, perhaps related to the relative load/processing times for JSmol and MathJax? Get the problem whether MathJax is loaded locally or from CDN.