Created Unassigned: Bundling does not seem to work after publishing with Visual Studio in v15.1 [27817]

I have an application that I've just updated to use v15.1 of the Ajax Contol Toolkit. I've also used the instructions on this page to configure bundling and everything looks good on my local machine.

https://ajaxcontroltoolkit.codeplex.com/wikipage?title=How%20to%20use%20bundling%20and%20CDN

If I inspect the source I can see a single script tag with src=/Scripts/AjaxControlToolkit/Bundle?v=<hash>.

However, after I publish the website through Visual Studio and upload the site to my live server, bundling doesnt seem to work anymore. Instead I see all the individual resources such as

<script src="Scripts/AjaxControlToolkit/Bundle" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/Localization.Resources.js" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/ComponentSet.js" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/Common.js" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/Compat.Timer.js" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/AnimationScripts.js" type="text/javascript"></script>
<script src="Scripts/AjaxControlToolkit/Release/BaseScripts.js" type="text/javascript"></script>

I've had a look around the net and various forums but I can't see anyone else having a similar problem. Any help would be greatly appreciated. Everything works, I'm just a bit funny about these things.