If it's not ginormous, can you just post it here in [code] tags?
But that click-to-activate looks really suspicious... IE does that with Flash and Active X sometimes... but plain ol' JS shouldn't, really.
Sitepoint has a popup that asks are you sure you want to log out? Which I normally don't see as I have JS off. So, they do it in a way that works with IE.
I suppose, just to be sure you don't have some wiggy security setting in your IE, can you verify that SitePoint's popup works for you in IE?