I was having the same issue. Implementing the workaround listed here fixed it for me: <a class="postlink" href="http://aspnetoptimization.codeplex.com/workitem/83">http://aspnetoptimization.codeplex.com/workitem/83</a>
Use this class instead of the stock CssRewriteUrlTransform class
public class CssRewriteUrlTransformWrapper : IItemTransform
{
public string Process(string includedVirtualPath, string input)
{
return new CssRewriteUrlTransform().Process("~" + VirtualPathUtility.ToAbsolute(includedVirtualPath), input);
}
}