What did you connect to the Line input? Channel gains (labeled "level" on the unit) were at 12 o'clock?
4 bars on the VU meter (set to ch1/4 or ch2/3) sounds about right, that's almost -3 db. Ideally it would be at 0db but depends on what unit did you connect to the line input (a CDJ would definitely give 0db)
Master knob was set at what level and how much bars did it show on the VU meter?
In Traktor you can see deck gains for each channel in the middle (enable it under Mixer layout-(filter+key+gain+pan+..). If you have the option of autogain selected Traktor will change gain of each track and it can be the reason why one song is louder:
Once you verify that is ok the last thing you can check is the volume control for channels and that is somewhere in windows setup for the mc6000 interface. Search for something like volume control.
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