One possibility is that the ~FULL_SPEED input pin is near ground level. If you have the pin floating it may be pulled near common ground. If this pin is at a voltage Low, all fans will be forced to full speed regardless of register settings. (One exception: Failed Fan Options/Sequential Start Register (14h) has BITS 3:2 set to 00b. This will set a failed fan output to 0% duty cycle regardless of the ~FULL_POWER value)
Drive or pull the ~FULL_SPEED pin High when the Full_Speed mode is not desired.