Chrome Version       : 59.0.3071.115
                     : 62.0.3176.0
OS Version: OS X 10.12.6

Test code:

<canvas id="canvas"></canvas>

<script>
  const canvas = document.getElementById('canvas');
  const gl = canvas.getContext('webgl');

  const testBlob = () => {
    requestAnimationFrame(testBlob);

    gl.clearColor(0.8, 0.5, 0.8, 1);
    gl.viewport(0, 0, gl.drawingBufferWidth, gl.drawingBufferHeight);
    gl.clear(gl.COLOR_BUFFER_BIT);
    gl.flush();

    canvas.toBlob((blob) => {
      console.log(blob);
    });

    setTimeout(() => {
      canvas.toBlob((blob) => {
        console.log(blob);
      });
    }, 0);
  }

  testBlob();
</script>

Expected:
Both blobs produced each frame should be purple.

Actual:
The blob produced inside the setTimeout is entirely blank, with alpha set to zero everywhere.

I can't get similar behaviour with a 2d canvas.