So I have begun to struggle with slow SATA speeds again. My old tricks didn't work, and I was looking for a way to test all of my hard drives in a equal playing field so I could isolate the problem properly. Which got me think about a RAM Disk. It's a pretty simple concept, part of your computer's RAM is used as a storage device similar to a hard disk. The upside is that it's orders of magnitude faster than any hard drive or SSD that you could possibly have. The downside is that if your power gets interrupted, everything in there is gone.
Ubuntu has a built in RAM Disk that dynamically resizes and will occupy up to half of you physical memory located at /dev/shm/. So, what I did was move a couple of Ubuntu ISO's to my RAM Disk and proceed to copy those to each of my hard drives. The result? I found out that it was my main system drive that was having intermittent trouble not my secondary drives as I had previously thought. I say this because sometimes it would perform admirably, other times it would be back down at 5 mb/s. I found a few ubuntu bug reports of this problem happening on and off on AMD 64 bit kernel versions for a while now and I have decided to give Ubuntu one last shot to get this fixed. I am going to do a clean install of 9.10 when it comes out. If the problem is fixed, hooray, if not, I will be looking into a different distribution. A problem like this brings my PC to it's knees on a regular basis and just flat out isn't something that should be happening with any linux distribution, let alone the most popular and widely used one.
*Update 10/10*
I have temporarily stopped Folding at Home from running, and the problem appears to have gone away.... Interesting. This demands more investigation.
*Update 2 10/10*
12 hours ago, everything was running, good, now it appears that my 5400 RPM drives are about 40% faster than my 7200 RPM drive...This is very weird. I may actually end up swapping the main system drive out when it comes time to upgrade to 9.10. I shall wait and see.
*Update 3 10/13*
I have decided that it's the drive itself that is going bad, so in addition to some fans, I ordered one of Samsung's new ECO green 500 GB drives as my system drive (newegg $50 shipped), and then when I RMA the 1 TB, I will just sell the replacement on ebay. That way I won't have to use the awful seagate drive that I have for anything other than temporary backup.