Hi Diego,
Can you send me a skin that causes the problem?
I thought maybe you were missing this from Web.config which is needed only under .NET 3.5
<tagMapping>
<!-- this tag mapping is only needed under .NET 3.5 to use the 3.5 version of the AjaxControlToolkit
Pages using controls from AJAX Control Tookit .NET 3.5 must use the ToolkitScriptManager, rather than the ASP.NET ScriptManager.
-->
<add tagType="System.Web.UI.ScriptManager" mappedTagType="AjaxControlToolkit.ToolkitScriptManager" />
...
</tagMapping>
The only thing related in the skin is the <ScriptManager in layout.master.
But if you send me the skin I can try to produce the problem here.
Best,
Joe