Hi Toshihisa-san,
I'm sorry for taking so long to answer your question.
From your spreadsheet, CASE 2 (Green) is correct. Maybe this physical description of what is happening will help:
The duty cycle adjustment is performed internal to the PHY, while the signal is still Single-Ended. The signal passes out of the PHY, to the Dual-DDR pad (special pad for differential pairs), where the Single-Ended signal is provided as an input to two buffer-gates in parallel: One buffer inverts the signal, and one buffer is non-interting. Since the duty cycle adjustment has already been applied, a setting of 001 will increase the duty cycle of the non-inverted signal by 1.5%, and will actuall decrease the inverted signal by 1.5%.
For your second question, yes, the two register effects are cascaded: the second cascade is applied after the first. They are cumulative, so that if both duty cycle controls are set to 001, the final adjust will increase the duty cycle to 53%. If one register is set to 001 and the other is set to 100, then the effects will cancel.
In practice, the actual change is applied by a fixed time delay of ~ 28 picoseconds on one of the clock edges, which will cause a 1.5% change at 528 MHz. The duty cycle change at 400 MHz will be closer to 1%.
Hope this clears this issue up for you.
Cheers,
Mark