I have this exact stereo (as does a friend of mine) - and no, no problems.

Have you played with the settings on the headunit? There's a subwoofer ON, as well as a subwoofer volume control(turn it to 15 - I'm guessing this is your problem, 15/15 is basically the equivalent to being at 0)
Of course there's also crossover settings that will really change the way things sound.