See http://tinyurl.com/37wfx2l (used TinyURL because I don't want anybody to think that I'm spamming my blog!)
The embedded Flash should be 640x480, but it's a tiny bit squashed. I thought that the ampersands in the width/height part of the href being encoded to & might be the culprit, but the plugin still seems to be picking up the height field.
It looks like it's only squashed by a few pixels, but that still messes it up. Any ideas?
What solved it for me was unclicking "Allow the prettyPhoto box to be resizeable" under "Appearance" in the Settings menu. My height/width worked just fine after that.
Settings menu? I couldn't find a settings menu, but what I did find and what worked for me was going into the js file and changing this line of code: allow_resize:true to allow_resize:false. That fixed the problem.