I have this exact same problem! I don't know how to solve it but I have come up with a work around.
The output to my headphones is recording on top of whatever audio input I am playing in. So the louder the audio output, the greater the impact it has on the recording.
Therefore, I turn the output right down and use my amplifier to ramp up the volume. This way I can still hear the backing tracks and metronome etc. but because the output from the IPad itslef is very quiet, it isn't audible in the recording. Would still like it to be fixed though!