I second this suggestion - it's what I use to make my SWF files iPod-viewable.I researched the heck out of this a while back and couldn't find an answer. I got Snapz Pro X with the second MacHeist bundle and screen capture seems to work the best.
You have to understand that a SWF movie (like StrongBad email) isn't like a .mov file or even .flv. It has layers to it.