Ahh right, must be slightly more technical than prettyPhoto then because if my memory serves me correctly, I only had a stylesheet to edit.
Then again I remember I had issues with the order in which I placed the <link> tags so maybe there was a <script> tag also.
Going to download PP again and take a look.
You seem to have much more of an idea about his code than I do so you're probably not far off realizing the problem.
Thanks for the clarification though.