I think you're looking at the wrong popups.
The
popup, popupHead, popupBody styles are for
text popups, not
topic popups.
If you insert a text popup (Insert > Text Popup), you should see your style changes.
A topic popup will display the topic as it is, using the styles of that topic.
The classes .MCPopupBody and .MCPopupBodyBG relate to topic popups, and are discussed here:
http://forums.madcapsoftware.com/viewtopic.php?f=6&t=5669