They've modified the server side markdown engine to not mess with stuff in math. We can't do this, so the double backslash gets converted to a single backslash. You could either use a quadruple backslash, or try to keep markdown from messing things up. Since we may migrate to SE 2.0, the most reliable thing to do is to enclose the align in P tags, like this:

<p>
$\begin{align}
2 + 3 & = 5 \\
2 \times 3 & = 6
\end{align}$
</p>

Try double dollar signs:

<p>
$$\begin{align}
2 + 3 & = 5 \\
2 \times 3 & = 6
\end{align}$$
</p>