What kind of popup window is it? If it is a Text Popup, you
should be able to change the color of the popup in the Text Popup
Properties.
If the popup is a regular topic, but it appears as a "pop up
window", you can right-click the topic in the WYSIWYG, select
"Topic Borders and Shading", and select a color. This color will be
applied to that topic only.
Hopefully that helps!
--Jessica