Arduino starts only, when programmer connected to USB.

Hello im new in the Arduino-World.
We are building up a school projekt with a Arduino Mega ADK.
Our plan was to build a AVR ISP2 Programmer in our device and leave it there.
So we would bring the USB Port of the Programmer to the outside and could connect our laptop to that port.
Now we have the problem, that our software on the Arduino only starts to boot, if a computer or laptop is connected via USB.
What have we done wrong, or what setting can i change to enable booting?
Thank You
Florian

Does the programer hold the reset line low? That will prevent bootloading from starting.