If I strip out most of the custom commands and package loading, then this is what I’m left with which still shows the problem:
\documentclass{revtex4}
\usepackage{amsmath}
\usepackage{colortbl}
\begin{document}
$\begin{bmatrix}
1 & 2 \\
\end{bmatrix}$
\end{document}
The problem seems to arise as a conflict between the revtex4 class and the colortbl package. Removing either one (either not loading colortbl, or using the article class) makes the problem go away.
There’s an answer by David Carlisle (who wrote colortbl) involving these two which is using the revtex4-1 class. I assume this is a similar but slightly newer version of revtex4. I find that using that makes the problem go away, so I’d recommend using that class if you can.
If not, wait until somebody who knows these packages/classes better to explain where the conflict lies, and what a suitable workaround might be.
colortblpackage; your example works without it. I'm not yet sure why this is though. – Ian Thompson Mar 21 '14 at 23:17\documentclass{revtex4} \usepackage{amsmath} \usepackage{colortbl} \begin{document} $$\begin{bmatrix} 1 & 2 \\ \end{bmatrix}$$\end{document}– jub0bs Mar 21 '14 at 23:20