Start of the long story:
My problems started 2 or 3 months ago, I thought the problem was hard drive issues until recently. It started out with a chirping/ticking noise coming from one of my hard drives and that drive disapearing from my computer. I did not test the drive in a desktop and just assumed it was a faulty drive, I then bought a momentus XT, I removed both drives and was only using the momentus xt, however I experienced problems with it, but found online that many others had issues with it as well. I wrote this off as the same problems everyone else was having. I did put this drive in my desktop and experienced the same issues in it. The drive would make a chirp noise and would then blue screen and crash windows or just lockup forcing a hard shutdown. I then purchased a ocz vertex which I placed in the opposite sata slot and installed windows 7 on it. I fought the momentus xt trying every possible fix posted on the seagate forums. I then tried both segate momentus drives in place of the momentus xt, both drives did the same thing. Yesterday I tried a western digital 320 gig drive that I know is good, it did the same thing as well (minus the chirp). I then decided to remove the ocz drive and put one of the original momentus drives into that slot, its now been 24 hours and my computer is running just fine.

So with the background story out of the way, what could possible cause one sata port to cause this problem? I do have the sata controler set to achi mode. I have tried many reinstalls of windows 7 as well as ubuntu and opensuse and experience the same issues every time. I am out of ideas to try, if anyone has any ideas I am all ears.