Ok, Looks like while using the settings in the bios set to full speed, the fan will work that way.
Also, if I have it on silent mode it will come on in about 15 mins after booting.
Now, if I go to set things in the Easy Tune settings everything get's messed up.
The fan stops responding and won't come back on unless I reboot and keep messing around with the settings.
I just want to have full control in my software so that I can set it to speed up according to the temps.
For now I am just letting it run off the bios and what's weird is, that I can use the settings in easy tune to control my exhaust fan and my cpu cooling fans without any issues, I am afraid that maybe later it will fail and not run those fans but it only seems that the system fan connections on the bottom are the only ones having issues at this time when any fan is connected down there.
Recently, while having the bios set to full speed or silent, I tried adjusting settings in the easy tune and it turned the fan off and told me that it was not detected.
If I move the RPM slider up and down and click apply, I can see the fan start spinning for about 2 seconds then it goes back off and that's when I get the error in the software.
Things are just not adding up to what is going on here, I am assuming the bios and controls are fighting with each other or something. I don't know.
Should not be this complicated to get some fans working when I have had no troubles with the entire building process while making this computer.
I tried requesting help through Gigabyte and it's been about 2 months now and I have never been contacted to get help with this issue.
Motherboard is still under warranty and all but I get no help.