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I started playing with a gamepad (Logitech f310) a couple months ago just fine, no extra software required. Make sure you have the controller plugged in before starting up Vindictus too, it doesn't seem to recognize if I plug mine in while the game is running.
edit: Missed the Nexon Launcher bit. I'm running with Steam, if my above tip doesn't work then the Launcher might be blocking the controller somehow.