I believe it is not just the size of font but the font itself should match.
Depending on your setting, the tex file generated by matplotlib
include preambles related with font setting. For example, below is
mine.

\documentclass{article}
\usepackage{type1cm}
\renewcommand{\rmdefault}{pnc}
\usepackage{helvet}
\usepackage{courier}
\usepackage{textcomp}
\usepackage{ucs}
\usepackage[utf8x]{inputenc}

And of course, the output is different from the output without these preambles.

So when you say,

On Fri, Feb 26, 2010 at 5:09 AM, Freddie Witherden
<fred...@witherden.org> wrote:
> Does anyone know what might be causing this? The document font sizes are the
> same and I tried to match the LaTeX file as closely as possible to the one 
> used
> internally by matplotlib.
>

Did you match those font preambles also?
Also, is it just the pdf backend? What about other backend?

Regards,

-JJ

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