This is more of a future request, then a question and is and issue I've seen with other plugin developers as well.
It would be great if you could adopt a best practice of using CSS elements that are uniquely named, such as WPMU-MessageBox or PopUp-MessageBox.
I've got an issue now where the theme I'm using has the same element name which unfortunately has an image associated with it. As a result, my Pop Up! boxes have the graphic element in them which really messes the formatting.
My only solution is to manually change the CSS element in the plugin or the theme which impacts the ease of future upgrades.
Realize, theme authors should do the same, but frustrating to deal with an issue that could be easily resolved with some best practice standards for unique element naming.