With the hundreds of classes used in SharePoint Portal Server and Windows SharePoint Services, there is no wonder there are some oddities when customizing.
One such glitch you may have run into when customizing the style-sheet is the side navigation bar links, more specifically the fact that they don’t always change even though you modified the link states for .ms-navheader.
The reason this is an issue is because the side navigation is contained within another wrapper which has the class .ms-nav applied to it (.ms-nav I believe is used for the links created when you create lists, libraries etc and they show up in the side nav). This .ms-nav class also happens to come “after” .ms-navheader in the style-sheet which means it over-rides it and is applied last. As you may have guessed the .ms-nav class also happens to have link states applied to it.
Luckily it really isn’t hard to fix, it’s a simple matter of moving the .ms-nav class “above” the .ms-navheader class in your style-sheet.
A more visual representation of the problem and how you can fix it.http://www.graphicalwonder.com/themeproblem.gif