@Kire this "problem" is unfortunately the desired behavior with this add-on because it is replacing what you type in between single $ in a latex document. @mindtouch: A better solution in general would be placing it between \begin{equation*} \end{equation*}. A short workaround to this is using $ in your equation yourself. so you start your equation with a $ which will end the mindtouch equation template and than you can use any latex command (well only basic ones and amslatex ones at this point), so e.g. \begin{equation} YOUR equation \end{equation} and at the end you again have to use a single $ to end the other side and get a correct latex file. This will then output a numbered equation with the desired behavior, Kire.