So the internet connection issue on start up, stopped and it's working properly now, maybe a Windows update or something fixed it, who knows.
I called MSI. First thing, I miscounted my SATA ports, I have 8 not 6..
Ports 1-2 are Intel 6gb/s
Ports 3-6 are Intel 3gb/s
Ports 7-8 are ASmedia 6gb/s
I have my SSD in port 1 and the two HDD's in ports 7-8. The RAID is done by Intel so I just had to swap my SSD and HDD's ports and I have it all set up and working good now.
Thanks for the help!