Win-7 multi-drive slow boot times

Hello all. This is the first time I've resorted to an online forum, so try to be patient with me. My PC has a newly acquired Samsung 840 pro. The 850 is my boot drive, and it is replacing a failed OCZ agility 3. Before the 840 arrived, I put win-7 on a seagate HDD. I want to use my seagate drive as a storage drive AND as a backup boot drive in case the 840 fails. Now...when I boot without the seagate drive hooked up to my mobo, boot time is 17 seconds. However, with the seagate drive attached, boot time is almost exactly 1 minute every time. It seems as though the priority is set to boot from the seagate. However, upon checking the "Samsung magician software," it recognizes the 840 as the boot drive and the seagate as a
"NON-OS-Disk," which indicates to me that the computer did in fact boot from the 840 pro. Furthermore, when I go into the UEFI-BIOS, and I go under "boot priority option," the 840 pro isn't even visible, and I don't think the seagate drive is either... My question is...what could be causing the slow-down when the drive is attached? Is there any way to have win-7 installed on two drives in the same PC, without causing any "conflicts"? That it possible to boot successfully from the 840 pro with the 17-second boot time, while still having an installed win-7 on the HDD as a backup option?
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    Yes it's possible to boot with two drives with same OS, first lets make sure you're booting from the 840, boot without the HDD connected, and once inside windows do some change like your wallpaper or something like that, so you know that one is the 840, then connect the HDD and startup your pc, see to which windows you get.

    BIOS should see both disks, maybe your mobo has different drive controllers and you're looking into the one that is unused, look around to see if there's another submenu for connected drives.

    Finally, assuming you get to boot into the 840 with the HDD connected and getting those 1min loading times, it could be that your pc is having issues recognizing your HDD, you might wanna run a chkdsk to verify its good status.
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