notebook renders equations with labels correctly on first execution, but not on reexecution

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If I open a notebook with the following content

## Important Part

It is well known <cite data-cite="Atr03">(?)</cite> that Spice grows on the planet Dune.  Test
some maths, for example $e^{\pi i} + 3 \delta$.  Or maybe an
equation on a separate line:


$$g(x) = \int_0^\infty f(x) dx$$

or on multiple, aligned lines:

\begin{eqnarray} \\
   g(x) &=& \int_0^\infty f(x) dx \\
        &=& \ldots
\end{eqnarray}

The area of a circle and volume of a sphere are given as

\begin{equation} \label{circarea}
A(r) = \pi r^2.
\end{equation}

\begin{equation} \label{spherevol}
   V(r) = \frac{4}{3} \pi r^3
\end{equation}

It is first rendered as:

But then if it is rerendered (i.e., going into editing mode and then rerendering the cell) it is then rendered as:

If one refreshes the page it returns to the first state (even with a soft refresh).

@gnestor @takluyver @carreau @minrk Why would there be a difference between the first time something is rendered and the second from a MathJax perspective? I know there is weirdness around this kind of thing for numbering equations, but as long as we aren't running into that I have no idea where to start thinking about solving this bug.