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It seems that since the last expl3 update (March 14, 2013), the flexisym package (used by breqn) is no longer compatible with the AMS document classes. Here is a minimal failing example:

\documentclass{amsart}
\usepackage{flexisym}
\begin{document}
\end{document}

This gives two Undefined control sequence errors at \begin{document}. Anyone have any idea what's going on?

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The fix should be on its way to the archives; meanwhile you can apply the fix suggested in this answer – egreg Mar 18 at 9:58
This is a 'known issue' and the code has already been updated on CTAN: should appear in TeX Live/MiKTeX in the next day or so. – Joseph Wright♦ Mar 18 at 9:59
Okay, it works now, with the updated flexisym v0.97c, dated March 16, 2013, on MiKTeX since March 18. – Ari Brodsky Mar 19 at 7:09

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