Hey I believe i know what you're experiencing. I have a similar thread I as searching for to mark as Solved..
In the properties of your game in C2, you have various options for letterboxing and so forth. Experiment with those settings to see if you can find something that would work best.
One of the options is called "Outer Scale" which I believe may provide the desired result.
So long story short, there are some properties in C2 that will likely influence how Cocoon wraps your game and displays on the screen.
In my case I didn't want any letterboxing. I wanted the project to go full screen but not stretch and that's where i had to use Scale Outer to get that effect.
Good luck!