Make sure you have this in your Web.config <httpHandlers section
<add verb="*" path="*csshandler.ashx" type="mojoPortal.Web.UI.CssHandler, mojoPortal.Web" />
It should already be there unless you had any conflicts with svn update.
To troubleshoot it I would view the source of the rendered page and see where it is getting its css from then view the css url in the browser to see the actual css.
Another setting you can try is
<add key="MinifyCSS" value="true"/>
You may try setting it to false. The Css is still combined but its not minified.
Hope it helps,
Joe
ps, I've got major changes to land in trunk tomorrow