Extra whitespace using google-code-prettify

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Hey I have a weird problem, I use the google-code-prettify code to display code on my blog, but somehow the pre tags don't really preserve the whitespace. For some reason, the whitespace is doubled and sometimes tripled when posting, making the code sections look awful. I use a local installation of the code, and my code sections are enclosed with:

<?prettify?>
<pre class="prettyprint">
    [code here]
</pre>

I have never had any issues with this before, anyone seen anything similar and know of a remedy?

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