Sometimes i found problems which "not sure why" causing some links on Joomla site don't work well. The latest issue that i found is about archive links that is not working when we setup the site to SEF from global configuration, it goes to 404 error page.
Of course i did find another issue also that is not far away different from this. Well, it's not really because the joomla development team missed out this, but actually it's just a simple problem. All you have to do is create a menu that is linking to the page. For example when i want to make the SEF link working on archive, i just have to create one menu link to archive component. And then all is working fine.
You must publish that menu, but you can hide the module position of that menu so this menu don't have to be seen on frontpage viewers/visitors.