Path Finder doesn't replace Finder as the default file browsing utility on OS X. When you need to open a file in an application, you'll still get a Finder window. If you click the "Open in Finder" button in folders on your dock, you'll still get a Finder window. Path Finder is just a standalone file browsing app, which annoys me. I really wish it would become the default file browser upon install, since it's a lot better than Finder.
UPDATE: This problem can be partially remedied by opening preferences window for Path Finder and going to "Reveal Preferences". There, you can set Path Finder as the default file viewer. However, you'll still have to use Finder when you're opening a file in an application.