Did you find any answer to your question?
I am also experiencing the Mute effect only on iPad whereas echo cancellation seems to work properly (without muting) on iPhone.
I met this issue also. this seems not an easy question, echo cancellation often works together with some "non-linear processing" module to achieve better EC performance. that means the audio level is adjusted non linearly and sometimes greatly suppressed if the algorithm thinks there should be only one person is speaking at one end alghought acutally there are voice from both ends.