Prevent Unity from auto-maximizing
How to keep programs from launching maximized? 11.04
Why do Firefox 4 and Evolution always open maximized in Unity? Even after you close the program windowed. Is this a bug?
Some applications will always open maximized in Unity. It's something to do with their initial size: if they take up more then X of the screen, they will be maximized (I'm not sure what's the value of X though).
There are two things to consider there.