An example of weirdness: I deleted the _latex folder and opened Mnemosyne. The 
first card displayed fine, then the second card I viewed displayed as follows 
(source on the right):

http://i.imgur.com/UQdufzC.png

contents of tmp.tex:

\documentclass[9pt]{article}
\pagestyle{empty}
\newcommand{\mathtiny}[1]{\mbox{\tiny $#1$}}
\newcommand{\ssub}[1]{_{\mbox{\tiny $#1$}}}
\usepackage{amsmath} 
\hfill\small  \normalsize\\
\setlength{\textwidth}{375}
\setlength{\parindent}{0pt}



\begin{document}
\frac{d^2}{dt^2}y(t)+2\zeta\omega_n\frac{d}{dt}y(t)+\omega_n^2y(t)=\omega_n^2u(t)
\end{document}



You notice not only is that TeX a bit messed up (\hfill\small  \normalsize\\ 
should not be before \begin{document}) but also this TeX is not actually from 
this card! Mnemosyne seems to have re-used the answer to the previous card as 
the question for this card. Hope this narrows it down a bit for you.

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