Ok, so take for instance the home page. If you clear cache, then hard-refresh on the home page. Any modules showing on the homepage will load in (section-1, footnav-1, footnav-2, footnav-3, footnav-4, footer). These will be the only modules that load in for the rest of the site now though. So when you navigate to the 'Homes For Rent' page, for example, you will not see the 'sidebar-r' module that is supposed to be there.
It's as if t4 is caching whatever modules are present on the first load, then not looking for any more modules on any other pages navigated to.