MikeR
Your explanation sounds like a phase issue, where i am guessing mono tracks (same audio for L & R)
would get cancelled and be completely zero volume and if you have any tracks the L and R aren't
identical you'll have some issues.
It could be an issue with whatever you're plugged into, mixer or whatever. I have had some of these USB adapters with the headphone out make issues.
To eliminate questions, run your iPad digitally into anything that could be used as an audio interface.
and then out to speakers or mixer properly in stereo. if your issue is no longer then you know
your problem is cable, adapter or both. also check whatever you're plugged into is panned L & R and not both those are centered.
EDIT: easy way to find out.
Bounce from your DAW an audio file, say a guitar (mono track) but with quite a bit of STEREO reverb.
on playback, if the guitar sound is gone but your reverb is on, its a phase issue.
