I have the latest bios firmware available.
I noticed that the problem occurs usually when I turn the PC on and at same time the Monitor is already on (the monitor is connected via hdmi to the discrete video card and stays in idle mode when my pc is off).
So I suppose that since sysfan_2 uses half the voltage than the other sysfan outputs (1 and 3), when I try to power on my PC with the monitor on then extra voltage is needed to wake the monitor from idle and this results to the sysfan_2 not to work, because it has less voltage.
In other words ther is no problem with my MB, but I think that the right connection of my second case fan (120mm) should be in sysfan_3 output and not in sysfan_2 as it is now.
What I cannot understand is how come they decided in gigabyte to make sysfan_2 with less voltage and not sysfan_3 instead???