You are trying to use alphaObj before it is fully loaded.
Try something like this:
var c1 = document.getElementById("canvas1");
var c2 = document.getElementById("canvas2");
var alphaPath = "http://eskarian.com/images/alpha-test.png";
var alphaObj = new Image();
alphaObj.onload = function () {
drawScene(mainColour);
addScene(colour)
};
alphaObj.src = alphaPath;
function drawScene(mainColour) {
var ctx = c1.getContext("2d");
ctx.drawImage(alphaObj, 0, 0);
ctx.fillStyle = mainColour;
ctx.fillRect(0, 0, 200, 300);
ctx.globalCompositeOperation = 'xor';
};
function addScene(colour) {
var ctx2 = c2.getContext("2d");
ctx2.drawImage(c1, 0, 0);
ctx2.globalCompositeOperation = "source-over";
ctx2.fillStyle = colour;
ctx2.fillRect(50, 50, 100, 100);
};