MSI Z87 GD65 dead/problematic sata ports

As the title says the sata ports on my motherboard seem to be screwing up. It all started when I went to plug in a possibly bad HDD to attempt to format it. After putting it into one of my hotswap drive bays in my 800D case and attempting to boot the system it seemed to just sit at the loading windows screen. So I tried restarting my computer without the potentially bad HDD in there and it was showing me as my raid 0 array as being bad since it wasn't sensing one of the drives in it. I thought that maybe one of my HDD in my raid array decided to quit but then I noticed I started having issues with my SSD not showing up in the system so I thought that very odd for a HDD and SSD to fail at the same time. So I pulled all 3 drives out of my hot swap bays and got different sata cables (power and data to see if the cables or little circuit boards that the 800D has for the hotswap bays went bad) and plugged everything in and it still wouldn't sense all my drives. After switching things around I discovered that port 8 was bad since the raid controller would say the array failed if I had one of my HDD plugged in there. So I unplugged everything and made sure of which ports were good and put everything back in the hotswap bays and the issue came back. So I tried running different sata cables to the hotswap bay boards and that made it to where my raid array wouldn't fail and the system would sense the SSD but it would just sit at the loading windows screen. So I took them all out again and have them back into the ghetto rigged setup of loose drives laying around and plugged in. I had to switch things around before I could get all the drives to be sensed again oddly enough port 8 is now working for my SSD. I flashed it to the latest MSI bios but that was about a month ago. If it helps the three drives I'm using are a OCZ Agility 2 and 2 Western Digital Caviar Blue drives. I don't want to attempt to see if that other drive that might be a lemon is working while my motherboard is screwing up.

Has anyone else had similar issues or have any ideas??
Sorry this is really long but I wanted to give as much info as possible and what I have already tried doing.

On a side note: I can also only push my i7 4770k to 4.3ghz at around 1.28-1.29V. I thought I just got unlucky in the OC lottery but could it be because this board might be deffective too?

Any help is appreciated.