Reduced Flight Time

I am flying a Cheerson cx-20 with ArduCopter 3.1.2 installed. When flying manually I typically get about 12-13 minutes of flying time. When I fly a mission programming it with Mission Player my flight time seems to be significantly reduced to maybe 10 minutes. Why is this? Is it because when flying a mission it is using more power to keep itself steady when going from one waypoint to another?

In a mission the speed of copter is fixed as defined in APM configuration when moving across way points. If this speed is more compared to when you were flying in non-mission mode, copter will draw more current and flight time will reduce.
You can change speed and increase flight time.