YOU ARE NOT DOING THIS CORRECTLY. THERE SHOULD BE A STEADY TONE (NOT MODULATED IN AMPLLITUDE) WHEN LISENING TO ONE CHANNEL ONLY THROUGH HEAPHONES. YOU ARE MODULATING BOTH CHANNELS IN AMPLITUDE WHICH IS A TOTALLY DIFFERNT EFFECT AND MODALITY.
Jeez, where were you 4 years ago? ;)
Binaural beats are working as long as you can hear the "wobble." The individual frequencies don't have to stay constant for that.
Mike Petroff