In lines 4-8, rather than:var user = new GlideRecord('sys_user_preference');user.addQuery('value', 'default');user.addQuery('name', 'my_home_navigation_page');user.query();Try:var user = new GlideRecord('sys_user_preference');user.addQuery('value', '...
Are the Theme and or Headers the same on the custom portal vs the out of the box portal?Could be a good starting point, if the custom portal has a different theme to switch it to match a working portal and see if issue remains
