I'm sure Eric will weigh in on this, but it has been my experience that poorly made Firefox themes visually screw up all types of my extensions that have a UI.
I'll agree with that. However, I might also take partial blame. Colors in the extension are all applied with styles (CSS). Firefox/Moz/NS define a number of built-in CSS classes which you're supposed to use in many cases instead of writing your own styles. There may be some places where I'm using inappropriate CSS classes or my own styles instead of the correct built-in class. Alternatively, it could just be a problem with the theme.
In order to check this out, I'll need to know which theme you're using (with a link to it) and whether you're on FF, Moz, or Netscape. I know little about how themes work, so I'll have to read up a bit on them, too.
-Eric
edit: nice home page. now when are you gonna help us with passwordmaker.org? :)