actually i'm not using a gigabyte board. i'm using an asus rampage III. i just posted a photo i found on google image search for ease of explanation.
thanks for saying its a good explanation... i do try.
well... the first thing i would check is to see if the fans actually are working. you could do this by plugging them directing into a molex using the adapter in the middle picture. most power supplies come with some sort of fan adapter. if they turn on then there isnt a problem with the fans.
next i would plug them back into the system slots and then start up some kind of game or demanding task. get some heat buildup. do the fans turn on?
if not try reversing the fan cables for the 2 which work and the 2 which do not. do the working and non working ones swap too?
go into your bios... look at your fan speeds and temps. does everything look right? if you dont have this option perhaps look into getting speedfan (a program) for when you boot into windows.
what was the problem with the fan controller your purchased?
link on another issue with your v2 fan controller. perhaps the fan controller is doa. do check if you have it plugged in to the psu first. remember you will need to turn the knobs to change fan speeds.
get back to us on your results to the above tests...