First thing to understand is that <asp:ScriptManager ID="ScriptManager1" EnablePageMethods="true" runat="server" /> declared in the layout.master is not part of the ajaxtoolkit at all, its part of the core MS AJAX framework in the System.Web.Extensions namespace. In 2.0 .NET this was shipped as a separate dll but in 3.5 its built in and no extra dll is needed.
The ajaxtoolkit does have a script manager that can be used instead of the normal script manager, I do not know whether using it would solve the problem for you.
You don't mention what version of mojoPortal you are using. There was an early version of MS Ajax that had a script manager that did not support page methods, so it makes me wonder what version of .NET you are using.
Hope it helps,