Sata ports on Mobo failing?

[Molsen1]

So for the past couple months my computer has been going downhill. It started with a few files randomly going missing, and sometimes the computer lagging when doing something while files were being found or read off the HDD. I would also sometimes find my computer to have gone blue screen after coming back from leaving it on for a little while like overnight or while at class. Also on occasion when trying to boot it would show that no system files were found. At first thought it was the HDD failing, and let it go for a while as I couldn't afford a new HDD.
Eventually I realized mine was still under warranty and got a new one, but that did not fix it. A little bit after having the new HDD I was still experiencing the same problems but worse, and even got to the point where I couldn't boot, as the computer wasn't finding a system file on the HDD. I ran some memory checking programs and tried booting with different sticks in and in different slots, but that didn't fix it.
I tried plugging my HDD into a different sata port and it was booted up fine and has worked for a couple weeks but again i'm now starting to notice missing files and occasional freezing and lag like I used to. So would it be a pretty safe bet to assume that my sata ports(and in turn the whole mobo probably) is going bad? I don't wanna replace another part that in turn isn't the problem.

 

[Slaymate]

The Southbridge on your motherboard maybe running hot in which case you can remove the heatsink, clean it and apply new thermal paste. The Southbridge heatsink is small and should be located in the bottom right corner of the motherboard (some older motherboards don't have a heatink on the Southbridge). If I knew the make and model of your motherboard I could probably find a picture showing you the location.

Of course this may not be the problem, but it might be.

 

[Molsen1]

The board is a Msi K9n Sli Platinum. Looking at the board I'm pretty sure I found it, and it sits right under my video card, so if it is getting hot that might be part of why. It felt warm when I shutdown and moved the video card but nothing too hot. I'm gonna let the computer run for a bit and see what kind of temp readings i get from PC Wizard.