The way you should imagine that it works: If board is mounted unlevel in copter or copter is not sitting perfectly level on ground, then when you start motors, the "top" motor does not need to run at all until it is flying and closer to perfectly level.
With motors running slowly on the ground, it will try harder and harder to make it level and so the "bottom" motor(s) will spin faster and faster. If you try to take off like this, it will flip before the bottom motors slow down enough. This is "PID-I term windup".
Knowing that it does fly and so the motor / prop directions are correct, etc. and assuming that you have default options set (not enabling always stabilize when armed, etc) (not even from some uav or cloud config), then the solution is that as soon as you start the motors, you should jump it up to knee-waist high instead of sitting on the ground and winding up.