3TB HDD Slows SSD Boot Time

My PC has a Intel Core i5-3570k processor on an Asrock extreme 3 Mobo.
8GB of Gskill Ripjaw Series RAM
Windows is on a Samsung 830 128GB SSD
2nd Samsung 840 pro
Running Windows 7 Pro

I recently replaced a 320GB HDD with a 3TB HDD in my PC.
After doing this i noticed that windows loads much more slowly.
I checked to make sure the 3TB drive is what was making the PC boot slow down by disconnecting the 3TB and rebooting, during the boot process before the colors for the windows logo fly in and come together my PC boots to the desktop, with the 3TB connected it takes about 90 seconds to boot into desktop.

The Samsung 830 SSD is still the boot drive, but i upgraded to the 3TB HDD for extra storage for games and movies. Since the HDD is over 3TB i used GPT file system to format the drive. I thought this may have been the reason for the slowdowns. I then tried to shrink the size of the 3TB into extra partitions and back up all the data on it to another partition so that i could reformat the first partition on the 3TB drive to regular NTFS and see if that would resolve the problem. After the first disk shrink it seems that even the original partition was automatically switched to NTFS reported from the My Computer page. Booting still takes about 90 seconds instead of what was about 10 seconds before the 3TB drive was added.

I have also taken the 3TB off the list of bootable drives and things in the bios with no gains.

Any ideas would be appreciated.
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