I am wondering if there is some kind of noise gate (then perhaps compressor) working. If you turn up the volume on your android device so it can detect the count well then a few other tests with the count's volume lower (you can use the volume control in the iReal Pro mixer) you might be able to hear what is happening.

Also you could save the audio file (with the count recorded) and play it from your android's music player, and change it's volume and see if it does the same kind of thing.