Can you please outline the scenario where you've observed this to be causing problems?
We have tested this today for another client's report and the functionality seems to work properly. For your convenience I'm pasting our reply below:
I have just verified this functionality to be working correctly on one of my local 5.1 projects, for your convenience please find below the source oft he control used for the test and a short video demonstrating the project behavior.
<%@ Control Language="C#" AutoEventWireup="true" CodeBehind="TestResourceLinks1.ascx.cs" Inherits="SitefinityWebApp.CustomLogic.Widgets.TestResourceLinks1" %>
<%@ Register TagPrefix="sf" Namespace="Telerik.Sitefinity.Web.UI.PublicControls" Assembly="Telerik.Sitefinity" %>
alert("jQuery not active");
On a side note you can use our ResourceLinks control to load your scripts as well, please note that it provides you with the ability of automatically combining embedded scripts from the same assembly. Please keep in mind that ResourceLinks loads scripts coming from relative paths, then scripts from embedded resources, and finally from CDN. Actually there would be no point using resourceLinks to load relative path scripts anyways, as it would be the same as using a <script> tag in your control masterpage.
the Telerik team
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