On my mediawiki installation, which is currently a few versions behind, I've had trouble getting MathJax to render when a JSMol instance is on the same page.
http://coco.sam.pitt.edu/~defusco/index.php/User:Albert/sandbox
After reloading the page several times it may just work, but it cannot be guaranteed.
If I use the Java Jmol applet everything appears to work fine.
http://coco.sam.pitt.edu/~defusco/index.php/User:Albert/sandbox?_USE=JAVA
I have added a section to http://wiki.jmol.org/index.php/Compatibility#MathJax_Compatibility_Issues covering this issue.