Jim, that is why your BD player (or any source) should always be set to the defaults, before you start a calibration. Some source adjustment may be needed, but most are a real pain and should be avoided. The biggest exception is the PS3.
Also, remember that the HC3800 (and other Mitsubishi PJs) clip the black level at Digital 16 (= Video Black), and the white level at Digital 235 (= Video White). Therefore, some of the setting recommendations for the brightness (Black level) and contrast (White level) do not work as described (the "below black" and "above white" flashing bars cannot be seen). I discovered this when calibrating my HC5500 for the first time.