I would check your layout.master and if it does not have this at the bottom of the <head> section, then add it there:
<portal:ScriptLoader id="ScriptLoader1" runat="server" />
and see if that solves it.
I would also compare some of the css files in your custom skin vs the newest versions of whatever you used as a starting point. There may be some aditional css you need to harvest and add to your skin.
Hope it helps,