Used True image WD edition to move up to bigger HDD, now old HDD is having issues

So, I needed to move up to a bigger HDD as one does when you run out of space, and I was going from a WD green 1.5tb to a WD green 2tb, everything seems to be working fine... save for one pretty big issue. Like an idiot I formatted the old HDD for storage purposes, and when I try to boot my computer it refuses to boot past the motherboard splash screen with the old HDD installed to a previously working HDD bay and Sata port. Windows will recognize the hard drive if I plug it in through one of my hot swap bays and I can format it, write to it, everything... until I shut down and then boot my computer up. If fact, it seems like no other previously working HDD's other than the newly cloned drive will allow the computer to boot... They will show up if I hotswap them in, but when I insert the 1.5tb HDD's start disappearing...

After a bit of digging the old 1.5tb HDD doesn't even show up in the bios when I can get it past the splash screen.

I have a M5A99FX Pro R2.0 MoBo with the latest bios, Amd FX-8350, 16gb Corsair Vengeance and a Sapphire R9 280x Vapor-X Tri-X, running Windows 7 Ultimate...

At this point I'm about to just reformat and start all over from scratch, but something tells me I should wait for more info in hopes that it isn't a new MoBo issue or something...

Update: I tried to pull the new 2tb HDD and see if the computer would recognize the old HDD in order to maybe re-install windows on the 1.5tb, and with only the old 1.5tb plugged in, I'm running into the same issue where I can't get past the MoBo splash screen... Not even into the Uefi Bios.

Update 2: I removed the 1.5tb and put the new 2tb back in with the other secondary HDD's that we're in the system before the clonening, and it boots just fine without any hiccups. Inserting the 1.5tb in different configurations still produces boot issues...

Update 3: I am now reformatting the old 1.5tb drive on another computer to see if that resolves any issues...