If you want to the POPFile UI to open in a new window (or tab) of your browser (instead of overwriting your current window), you will have to adjust the settings of your browser or operating system. POPFile itself cannot do anything about the way the link to the UI is opened (at least not in a cross-platform, cross-browser way).
In the Firfox menu, choose Tools → Options, switch to “Advanced” and find the “Tabbed Browsing” section. Here you can control how links from other applications (including the operating system) are dealt with: you can have them opened in the current tab of the current window, in a new window, or in a new tab in the current window.
Use the Control Panel to open the Internet Options applet. Switch to the Advanced tab and search for the “Open links in same window” option. Make sure the option is not checked.
Opera doesn't allow you to specify how links from external applications are handled. But it does give you the global option to “Reuse existing pages” (Preferences → Windows). If you uncheck this option, new links (either from POPFile, your bookmarks, or some other application) will be opened in new tabs or windows. You can control whether you want new tabs or new window with the “Window handling” option.