Matt, You are definitely missing something simple as CSS has always need to be compiled to a SWF. Just right click on the CSS file and choose compile to SWF if you have not already. There has been some minor changes to CSS in Flex 4 and that is what you are running into with the namespace issue. If you are attempting to use a CSS file that you had working in Flex 3 now in Flex 4 than you have to add namespaces like this at the beginning of the file
/* CSS file - Standard Stylesheet */
@namespace "library://ns.adobe.com/flex/spark";
@namespace mx "library://ns.adobe.com/flex/mx";
@namespace esri "http://www.esri.com/2008/ags";
@namespace viewer "com.esri.viewer.*";
@namespace MapSwitcher "widgets.MapSwitcher.*";
@namespace components "com.esri.ags.components.*";
and then use those name spaces like this:
mx|Alert
{
background-alpha: 0.8; /* same as for viewer|WidgetTemplate */
background-color: #000000; /* controls the panel content area. */
color: white; /* main text color */
corner-radius: 10;
title-style-name: "myAlertTitle";
}