You need a slight modification to your code if you are packaging as an app. You need to make sure that the main fuction which you package returns a figure handle so that the app removes itself from the path when you close it.
it doesn't work in matlab R2012 a. I get:
Error using load
Unable to read file sprites2.mat: No such file or directory.
Error in flappybird/initVariables (line 276)
Sprites = load('sprites2.mat');
Error in flappybird (line 94)