Commented Unassigned: issue with bundle [28013]

I am upgrading from version 4.0. The upgrade worked fine. However i am having issues with resource bundling.
After installing the web optimization & static resource, I still do not see the bundle at the refer path
<asp:ScriptReference Path="~/Scripts/AjaxControlToolkit/Bundle" />

Did I missed something?
Comments: Would you please provide a sample project that illustrates this issue? For example, you can remove production code from the real project and leave minimal code that shows the described problem.