Ashley, I know you probably did, but you may not have if you were in a hurry, but did you see this part:
Remove the HTML entry point file.
The following list shows all the HTML5 functionalities that the current version of CocoonJS supports. If you are using any other than these, you won't get the expected results but it doesn't mean your application won't work.
using dynamic canvas as a drawing texture
OpenlAL based multichannel Audio
webkitRequestAnimationFrame, setInterval, setTimeout, alert
In App Purchases
Social networks integration
Locking device orientation
Suspend and Activate callbacks
Automatic antialising and full screen scale
All path segments: bezier curves, elliptical arcs.
Fill and gradients