Whether it is flipped or not seems to depend entirely on how it ended up being shuffled.

Maybe that's why you don't use Javascript Math.Random() for cryptographic purposes? :-)

Shuffle function:

  function doShuffle() {
    var startTime = Date.now();
    var pixels = shuffledImage.data;
    while (shuffleStartColumn < width) {
      // Pick a random column j in the range [i, width) and move it to position i.
      // This Fisher-Yates shuffle is the less efficient than the Durstenfeld shuffle but more animatedly appealing.
      var i = shuffleStartColumn;
      var j = i + Math.floor(Math.random() * (width - i));
      for (var y = 0; y < height; y++) {
        for (var x = j - 1; x >= i; x--) {
          var off = (y * width + x) * 4;
          for (var k = 0; k < 4; k++) {
            var temp = pixels[off + k];
            pixels[off + k] = pixels[off + 4 + k];
            pixels[off + 4 + k] = temp;
          }
        }
      }
      shuffleStartColumn++;
      if (Date.now() - startTime > YIELD_AFTER_TIME)
        break;
    }