Did you manage to control the speed of system fans on sys_fan2 and sys_fan3? I've got this mobo - sys_fan1 and cpu_fan work fine and I can control the speed but sys_fan2&3 contantly run at 100% regardless of bios setting. I've got a call open with Gigabyte for this.
From page 6 of the review:
Once again, if you're Windows user, a better fan control experience is available in the form of SpeedFan. Properly configured, it can control all three fans, though SYS_FAN1 only works with voltage control (3-pin) and the same control is tied to the voltage of CPU_FAN. To enable the fan controls, find the "IT8728F" chip in the advanced menu and change its PWM 1-3 modes to "software controlled."
We also discovered through trial and error that the temperature Gigabyte specifies as "System" corresponds to the area around the VRMs to the left of the APU socket. This is a good location for a temperature sensor as the circuitry in that location runs quite hot and lacks cooling aside from any spill-over airflow from the CPU fan.