Make sure you have this in the head section of layout.master file in your skin:
<portal:ScriptLoader id="ScriptLoader1" runat="server" />
The ScriptLoader will include the jquery and jquery ui scripts so you do not have to add them yourself. Since you upgrded from a very old version, you may want to look for other differences in the included skins under /Data/skins and compare to your skin to find new css or new things in layout.master.
Hope it helps,