The change apparently came in the midst of a consumer study showing a large fraction of VG consumers who were not aware that "Modern Warfare 2" was a CALL OF DUTY title.
http://www.joystiq.com/2009/07/09/activision-modern-warfare-2-was-always-ready-for-the-call-of-d/
http://www.joystiq.com/2009/07/21/interest-in-modern-warfare-2-spikes-with-call-of-duty-branding/
Note that it isn't called "Call of Duty 4 (or 6): Modern Warfare 2". That would get confusing.
The official box art: http://img197.yfrog.com/i/ia1n.jpg/
Amazon has updated the title but not the box art, yet ...
http://www.joystiq.com/2009/07/09/activision-modern-warfare-2-was-always-ready-for-the-call-of-d/
http://www.joystiq.com/2009/07/21/interest-in-modern-warfare-2-spikes-with-call-of-duty-branding/
Note that it isn't called "Call of Duty 4 (or 6): Modern Warfare 2". That would get confusing.

The official box art: http://img197.yfrog.com/i/ia1n.jpg/
Amazon has updated the title but not the box art, yet ...