I think it's the motherboard's flaw because:
1) If it wasn't then the USB3 disk wouldn't work in my laptop also.
I have tested the USB3 (how much voltage does it needs? a simple passport) on the battery only with the laptop.
It works fine again.
2) At the new motherboards (X79) Gigabyte has replaced Etron with Fresco controllers.
I don't think this is coincidence.
They understood that there were problems with that chipset and they did replace it with another controller.
Only the users have been left out with a problematic controller.
3) It wouldn't be a problem if it wasn't working at all or even partial.
BUT the motherboard sees the Passport ONLY after I unplug it and plug it again AFTER booting in windows.
The light of the Passport is ON which means that it takes the power but it can't be discovered in windows.
I think this is a controller (maybe controller/driver) issue.
4) The same Passport works fine into a USB2 port.
5) Some times it takes more than 4-5 times to be discovered after I unplug it and plug it those times.