Javascript FileReader reads file incorrectly

I have a short JavaScript function which will take an uploaded file and display the hex equivalent of it. Comparing the original file and the output in a hex-editor shows that they are partially different but not completely.

String.prototype.hexEncode = function(){
  var hex, i;

  var result = "";
  for (i = 0; i < this.length; i++) {
    hex = this.charCodeAt(i).toString(16);
    result += ("" + hex).slice(-4);
  }

  return result
}

function upload() {
  var file = document.getElementById("fileToUpload").files[0];
  var reader = new FileReader();
  reader.readAsText(file, "windows-1252");
  reader.onload = function (evt) {
    var program = evt.target.result.hexEncode();
    program = program;
    console.log(program);
  }
}

Here are the original file and the output next to each other:

2A 2A 54 49 38 33 46 2A 1A 0A 0A 43 72 65 61 74
2A 2A 54 49 38 33 46 2A 1A AA 43 72 65 61 74 65

What is causing the difference in outputs? Any help would be greatly appreciated.