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Rooted, but how do I use superuser?

Ok, I assume that whenever I open an app it is supposed to ask for su privileges. The only problem is that when I open an app, nothing happens except the app opening normally. The app does not ask anything about superuser. Only rootchecker asked to allow su privileges. No other app will do this when I open it including all backup. Rootchecker says my phone is rooted, but the apps are not recognizing su evidently.
 
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