This happens when changes are made and redirecting to other pages especially during login or logout. Code for ondevice ready is,
document.addEventListener("deviceready", onDeviceReady, false);
function onDeviceReady() {
//alert("ready");
navigator.splashscreen.hide();
window.onbeforeunload = null;
}
Please suggest a way to hide this native pop up..
Add the following line in your code,
window.onbeforeunload = null;
This line need not be placed inside deviceready event listener. It can be placed on functions that it called during click of back button or during page reloads.