Using 3.5.3 I have created the Main Menu using WP Ver 3.0.4 Menu Function and this displays properly, see http://www.yourultimateresource.com.
I have installed 3.6.1 as a seperate Theme (see
when activated it pulls in 30 of the 44 "Published" Pages (not sure if there is a 30 menu item limit in WP).
Looking at the WP Menu Set Up page, this still shows the original SetUp which is shown in 3.5.3.
Does anybody have a solution to this problem?