Thanks for posting this, I had the same thing happen because I was adding a CAShapeLayer to my window for a gradient effect. Your post helped me figure out that this was the problem.
It looks like this is happening is because they are adding their view's layer to the window's sublayers--at index 0 I might add! This is contrary to what you would expect, which is that they would add their view as a subview to the presenting view controller's view.
They must have just thought that people don't add layers to their window and they want to make sure they are not competing with your view stack. Why they would put it into index 0 must only be because someone is in the habit of doing -[CALayer insertLayer:layer atIndex:0]
I suppose.
I'm not certain but I am guessing this could be the case with any modal view controller.
The fix is pretty simple:
[viewController presentViewController:facebookViewController
animated:YES
completion:^{
facebookViewController.view.layer.zPosition = 1000;
}];