This issue is also present on your demo site and has the same behavior. When clicking on some of the pages (for example Responsive), and then clicking on 'login', it gives a 404 error page, but it works fine from the Home page and other pages.
I did notice that some of the template path is being appended to the middle of the link in the browser, when the 404 errors appear (on your demo too.) For instance, a working page (like the home page, when clicking on 'login') goes to:
http://www.shape5.com/demo/design_control/index.php/component/users/?view=login and that works fine, but the broken pages append a middle path to the link (which if removed, the login link works fine), so an affected page (like Responsive, and when clicking 'login') looks like this:
http://www.shape5.com/demo/design_control/index.php/features-mainmenu-47/template-features/index.php/component/users/?view=login (notice the appended path in the middle of the link causing the 404 error page: "features-mainmenu-47/template-features/" )
How can I resolve this so that all pages 'login' link works correctly?
Thank you in advance.