You shouldn't just lower the brightness control to darken the picture, unless it's set improperly. Brightness should be set using a pluge / black clipping pattern and left alone. D-Nice's setting should be the correct setting (or close to). If you want more or less shadow detail, you're better off adjusting the gamma.
And D-Nice's settings shouldn't be mistaken for a real calibration... they're just settings that should work better than the out of the box settings. When you calibrate a set, you normally leave it alone after. Some sources look over-saturated, some look washed out, some have poor black levels... you'll drive yourself crazy if you tweak the picture for every source.