I do recommend turning off the multi-route audio setting if you aren't using multi-route audio. That is only needed if you are using a USB audio interface and you want to send one audio signal to that interface and a separate signal to the headphone jack. Turning this on makes some big changes to the audio functionality on iOS, so I can imagine that causing the problem.
Can you confirm that the problem only occurs with multi-route audio turned on? The other audio settings probably don't matter. Then I will follow up with IK Multimedia to clarify that the problem only occurs in multi-route mode.