Old hard drive won't allow boot now

So, here's what started. I noticed that I was having a boot drive issue a few days ago. My boot drive was set to the wrong drive so I couldn't format the 2nd drive that was starting to fail that had the boot information on it. I proceeded to look up some information on how to fix this considering just taking out the drive would cause me to not be able to boot again. So I copied all of the boot folders and files over to my SSD that somehow didn't get them when I reinstalled after installing it. I had not restarted my system since that point for a couple of days I believe.

Today my system had not yet still been restarted but I received in the mail a USB to notebook-sata/memory card reader, internal. I get all excited and start tearing in to my system. I get it all connected and start it up but there is an issue with my boot files. Since I had read about this a few days before, I unplugged all of my drives except my SSD and put in the windows disc to do a start-up repair. Got it working just fine and got in to windows. it even recognized and installed the drivers for the card reader. Everything looked good (except of course all my desktop information missing since that drive was disconnected).

I plugged all of the drives back in and the computer wouldn't get past the windows logo. Here is the configuration that is bothering me:

Drive 1, SSD Sata - Healthy, Working fine now with all boot data

Drive 2, 1tb Sata - Healthy and has my docs on it

Drive 3, 640gb sata - Healthy via S.M.A.R.T. but system won't get past the windows logo when plugged in

Drive 4, 1tb Sata - Old drive with boot information on it but allows system to boot just fine whe plugged in, also, s.m.a.r.t. detected as beginning to fail.

Drive 5, 1tb sata - Another healthy drive and boots fine with the system

I am running windows 7 x64 ultimate with all updates and updated drivers and firmware.

Gigabyte mobo GA-790fxta-UD5 chipset

Radeon HD6950

4 x 2gb DDR3 1600

Phenom II 965

1000 watt psu

Now before you say something about power consumption, why would it be that the 640 gig won't allow it to boot but replacing it with the 1tb that smart says is failing, it boots just fine.
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  1. One last thing, the drive that won't allow it to boot is a Seagate Barracuda 7200.12

    Also, the system runs just fine when I use the seagate via a hotswap bay once I get in to windows.
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