
Try this...
Play audio on channels 1 and 2
Disable the crossfader
Take the CH1 fader up, CH2 fader down
Set the headphone mix knob to 12 o'clock
Press the master cue button - you'll now hear the audio in your headphones, the same as your master output
Press the master cue again to disable it
Press the CH2 cue button - you'll now hear THAT audio in your headphones, CH1's audio is still in the master output
Press the master cue so both CH2 and master cue are illuminated - you'll now hear both the master and CH2 in your headphones
Turn the headphone mix knob back and forth between master and cue and you'll hear it blending between the master and CH2 sources
Turn the headphone mix knob back to 12 o'clock
Press the CH2 cue so only master cue is illuminated - again, you'll only hear the master in the headphones and master output
Raise the CH2 fader so both CH1 and CH2 are open - you'll now hear both sources in the headphones and master output
Press the CH2 cue button and you'll find it's now louder than the CH1 source in the headphones because you're mixing it twice; once from the channel, once from the master
Turn the headphone mix knob back and forth between master and cue and you'll now hear the master mix of both channels and then CH2 in isolation
From what you've written, I think perhaps you misunderstood the way the channel and crossfaders work in relation to the headphone cueing.