When I host an application in a subdirectory (say, localhost/myapp) and I set web.config debug="false", CSS urls are made absolutely relative to the site root rather than the application root.
Consider this config:
.Include("~/Content/2012.2.607/telerik.metro.min.css", new CssRewriteUrlTransform()));
telerik.metro.min.css includes url(Metro/Sprite.png). The result of CssRewriteUrlTransform is that such URLs are rewritten to /content/Metro/Sprite.png instead of the correct /content/2012.2.607/Metro/Sprite.png.
CssRewriteUrlTransform.Process contains the following code:
return CssRewriteUrlTransform.ConvertUrlsToAbsolute(VirtualPathUtility.GetDirectory(includedVirtualPath.Substring(1)), input);
Since includedVirtualPath must start with "~/" (as far as I can tell), this causes the absolute path issue. Removing .Substring(1) seems to work fine.
I'm using 1.1.0-beta1 prerelease package in NuGet.