I also added a link to the "www.mysite.com" popup to close the window:
<a href="#" onclick="window.parent.Shadowbox.close();" style="float:right"/>Close Window
The "Close Window" link works on my laptop, in both Firefox and Safari, but does nothing on my iphone or ipad. I can close the window but clicking outside of it, but that's not the solution I want. I'm not sure what the problem is.