The full process of calibration in WriteInstinct.ino is:
1. You don't know where the servos are pointing at before calibration. So you don't attach the legs.
2. Upload skills, which include one "calib" posture, it's a posture with all joints at zero position. There's also a "rest" posture. Of course, you won't see the postures because you haven't attached the legs. But you can imagine that the servos will rotate when switching between the two postures.
These postures are also shown in 6.4.3 of the instruction document.
You have to enter 'Y' for saving saving skills to EEPROM. Right after that, the program will read the rest posture and rotate all servos to rest position, then shut them down to avoid vibration. Still don't attach the legs.
4. The program will ask you whether to calibrate MPU. You can enter 'n' to skip if you have already did so. You can now understand why I put Nybble to rest state before calibrating MPU. It's much easier to lay Nybble level on the table, and it won't vibrate due to the shaking of servos.
5. Now if you enter 'c', the program will read the calib posture and execute. All the servos are supposed to rotate like crazy (but they are actually transforming from rest position) until they stop at calibrate position. Then you can attach the legs one joint by one joint, perpendicular to nearby references on frames. It's easier to attach knee joints before shoulder joints.
Even if you attach legs in the direction of calibrate posture before entering 'c', the servos are actually in rest posture. Once you enter 'c', the legs are going to move, but would probably hit something in the middle. In that case, the motor will be forced to stop, and becomes a pure resistor. It will pull large current, generate heat and cause a voltage drop on the chip. That will further disturb the signals, causing more abnormal behaviors.
6. After attaching all the joints, Nybble will stand on its knees as in the calibrate state. The directions of legs won't be perfect. Use the included L-shape tuner for fine tuning each joint. You can enter 's' after calibrating each servo in case of any interruption in the process.
7. The calibration values are saved to ATmega328P's onboard EEPROM. They won't change unless some voltage shock happen to cause "bit flip" when the processor is accessing the memory location. But it's very rare. Next time you want to calibrate, you don't need to take off the legs. You can also calibrate within Nybble.ino.