Problem with matplotlib and pdflatex

I'm trying to use some matplotlib-generated pdfs in a pdflatex document,
and seeing some extremely weird and disruptive size effects. The
resulting pdfs can be seen at

http://research.janelia.org/coventry/paper.pdf
http://research.janelia.org/coventry/paper-small.pdf

The first results from the code

\begin{figure}
  \centering
  \subfigure[Prior distribution]{\label{fig:prior-graph}
    \includegraphics[width=6in]{prior-example}
  }
  \subfigure[Posterior distribution]{\label{fig:posterior-graph}
    \includegraphics[width=6in]{posterior-example}
  }
\end{figure}

and the second from the same code with "width=5cm". The two pdfs I'm
trying to include are at

http://research.janelia.org/coventry/prior-example.pdf and
http://research.janelia.org/coventry/posterior-example.pdf

It doesn't matter what order I include them in, I get the same size
effects. If I generate postscript files with matplotlib and convert
them to pdfs, I don't get this problem. So I have a workaround, but I
would like to know how to create usable pdfs directly, and thought
reporting this might be useful to matplotlib development.

Best,
Alex