zulip: bugdown: Latex shifts superscripts and other offset characters downwards.

To reproduce, send a message like

Subscripts and superscripts: $$a^X B^X a^x a_X B_X$$. 
\frac: $$\frac{a}{b}$$, \over: $${a \over b}$$ and \bar: $$\bar{\theta}$$. 
Integrals: $$\int_0^1$$.
This seems to be okay: $$a^{a^{a^a}}$$.

The frontend markdown processor is doing the right thing, but the backend markdown processor returns:

I would start by figuring out what is different between what the frontend and backend markdown returns. http://zulip.readthedocs.io/en/latest/subsystems/markdown.html is useful reading.