Some HTML Tags are stripped from extension output on betalabs even though the "markerType" => 'nowiki' is used to prevent the output from further modifications.
This problem does not happen on my local vagrant test instance.
The concrete example that can be seen on http://deployment.wikimedia.beta.wmflabs.org/wiki/User:Anomie/Sandbox
if visited as logged in visitor with MathML rendering option in your user preference section is reported as BUG 66495. But I don't know if the bug is related to the Math extension or some other effect.