Hm... The author has this example on his page:
<a href="http://www.adobe.com/products/flashplayer/include/marquee/design.swf&?width=792&height=294" rel="prettyPhoto[flash]" title="Flash 10 demo"><img src="images/thumbnails/flash-logo.jpg" alt="Flash 10 demo" width="60" /></a>
So try to use rel -> prettyPhoto[flash], maybe this does the trick
http://www.no-margin-for-errors.com/projects/prettyphoto-jquery-lightbox-clone/Edit: Ah! The version 2.5.6 seems to be too old for jQuery 1.4.4. Download the current version from the page above and replace the file jquery.prettyPhoto.
js in the js directory. Fixed this for me.