Here's a possible solution for those having flickering problems, namely one that occurs whenever the game changes layout:
CocoonJS does not support letterbox scaling and if you try it, CocoonJS will default to Scale outer for fullscreen. If you use Scale outer with Construct 2 however, and you do not use the Scroll to behaviour anywhere in your project, then every time the game moves from one layout to another, Construct2 first puts everything in the middle of the screen for the first frame(s), then moves it all to the left side, resulting in a jarring flicker.
The way to fix this is simply add a Scroll to (0,0) call to the start of each layout.