There seems to be some issues when combining MathJax and jQuery Mobile on the same page. Sometimes the MathJax renders correctly and other times it does not - and this can happen to the same page.
The HTML that loads both of them looks like this:
<script type='text/javascript' src='http://code.jquery.com/jquery.min.js'>
</script>
<script type='text/javascript'
src='http://code.jquery.com/mobile/1.0a4.1/jquery.mobile-1.0a4.1.min.js'>
</script>
<link rel='stylesheet' type='text/css'
href='http://code.jquery.com/mobile/1.0a4.1/jquery.mobile-1.0a4.1.min.css' />
<script src='/beta/mathjax/MathJax.js'>
</script>
You can see an example page here: http://stackmobile.com/beta/math.stackexchange.com/questions/view/?id=47772
Edit: It seems to be a problem with MathJax not recognizing a new page being loaded via AJAX - here is an example that doesn't seem to work: http://stackmobile.com/beta/#/beta/physics.stackexchange.com/questions/view/?id=11678