The callback function will be launched immediately after the “resume” if the user comes from a notification.
So, I would handle your case as follows:
, , (a la var is_paused = false; ).
is_paused true "" Ti.App - (1 ) Ti.App.
, , is_paused var :
//in notification callback
if(is_paused){
//user is coming from background (do your thing automatically)
}else{
//user is in app (display the alert)
}