possibly broken fan header/regulator.
before I have broken numerous sys_fan plugs, and they all stop working. The controller for these is seperate from cpu_fan.
I have broken them by either connecting too many fans, using external speed regulators with them etc.
It is not normal, and not particularly safe either since the fan speed will be regulated based on chipset temperature, and not CPU temp. Safest thing to do would be to set bios fan control to off, so that it spins at full speed.
do contact gigabyte for a replacement