Hi Alex,
Thanks for sending your skin so I could see what was going on.
The problem is that <portal:Scriptloader must have the id="ScriptLoader1", in your skin you have changed the id, so it cannot find the ScriptLoader by its expected id therefore it adds another instance of scriptloader control and this causes it to render those duplicate scripts at the bottom.
You can solve it by setting the id="ScriptLoader1" like this:
<portal:ScriptLoader ID="ScriptLoader1" runat="server" />
Hope it helps,
Joe