As far as I learned from this topic, both CSTheory & MathOverflow use MathJax. In addition, when I checked the version, I noticed that both use v1.0.1.
However, the math rendering experience is quite different on TCS & MO: while the former takes a (considerable) time to render a formula, the latter works on the fly (especially while entering a question or answer).
Is there a reason behind this?