OK, I don't quite understand why this is, but after spending a bunch of hours on this I finally came across someone who had a similar issue (Post). The fix is to ensure the ToolkitScriptManater has the CombineScripts attribute set to false. For example:

<ajaxToolkit:ToolkitScriptManager runat="server" ID="ajaxScriptManager" EnablePartialRendering="true" CombineScripts="false" />

Hope this helps someone else