Ok, I did figure out the I/O read errors (had to format in exfat, windows 7 backup doesn't like sector sizes above 4,000 bytes). However, even when I put in the other drive (2 tb eagle) its not recognized in the usb 3.0 slot. Weird thing is, I have put these 3 tb usb 3 drives on another machine and presto they are instantly recognized in the usb 3.0 slot. With that being said, I'm beginning to think its either a driver issue or something else. As I have stated before, I did update the usb 3.0 drivers to the latest ones as this was still happening when I was using the default usb 3.0 drivers that came with the motherboard.
Update: Something else was a little off, when I tried to do a copy from one drive to the other (both 3 tb) the other drive would drop its connection and was still flashing when I came into work this morning.