Your flow of control does not waitfor() or uiwait() after creating the graphics, so you get to the bottom of the initialization loop and exit the program.
When you do not compile, then the graphics objects all keep existing because you have the keyboard to go back to for more interaction.
If you are using GUIDE, then look in the code generated for the GUI OpenFcn callback, and you will see a commented-out call to wait for the graphics window to close. Remove the comment marker so that wait becomes active.
