First off, thank you for developing a really clean, simple, well-documented product. I'm building a portfolio for some websites my company has designed using Joomla. The websites show up in a shadowbox, but for some reason, in Firefox 2, any swf flash (not flv) within the website that is contained in the shadowbox seems to be suffering some kind of redraw problem.
Originally, I was actually trying to incorporate shadowbox into the joomla sites which are displayed in the portfolio, but they suffered the same problem in Firefox when trying to display Youtube videos and the like.
I have not had any issues getting shadowbox to display flash content. What I did was create a page to output the embed code and I link to it with shadowbox. So in essence, its not just flash content, but that is all that is rendered on the page.