Good news! My project is working like it should now.
I'm still not sure what the problem is but I would recommend not to copy the c2runtime.js file, the images, and the media files to the template project and test the game with it. Even though I have edited all namespace, references.... to match my project, the bug still persist.
So I decided to use the default project, exported by the engine, and copy over the necessary codes that I use (mainly in the MainPage.xaml.cs), and it is working! :)