rotary encoder strange behavior (too many datas)

Sorry - I thought from the above that you may have sorted it... Espruino does actually include the ability to monitor a pin in a setWatch, so that may help you:

var value = 0;
setWatch(function(e) {
  if (e.data) value++ else value--;
  print(value);
}, A5, {data:A8, repeat:true});

I notice you're doing a print and digitalPulse. Is it possible that turning the knob quick is creating so many events that the functions can't be called quick enough and so it loses track?