HDD is incredibly slow after reinstalling Windows on SSD

I had to reinstall Windows 7 Home Premium x64 on my SSD, because it didn't boot properly. I decided to make a clean install. When I chose to install Windows onto the SSD, it told me it couldn't install to the specified location. When I plugged out my HDD, it worked.

When the Windows installation finished, I tried plugging the HDD in again. It seemed that Windows was unable to start. I tried waiting, and instead, the Windows loading time had increased from 2-3 seconds to 2-3 minutes. The HDD is running incredibly slow. Here is some benchmarks:








Here is the information Samsung Magician gives about the HDD:

Code:

PHYSICALDRIVE4:
            Model Name    ST3000DM001-1CH166
            Manufacturer    ST
            Firmware Version    CC26
            Size    2795GB
            Max LBA    5860533168
            ATA Standard    ATA8-ACS
            Word Wide Name    5000C50050932F09
            Multiple Sector    16

            Partition1:
                Partition Type    MS Reserved Partition
                Start Offset (MB)    0
                Partition Length (MB)    128

            Partition2:
                Partition Type    Primary Partition
                Start Offset (MB)    129
                Partition Length (MB)    2861458

            Volume G:
                Volume Type    Games and Storage
                File System    NTFS
                Total Size (MB)    2861457
                Used Space (MB)    2086015
                Free Space (MB)    775442
                Free Percentage    27.10

I have no idea what the problem is. It has never been as slow as this. Copying files to and from the HDD takes forever, and playing games stored on it doesn't work well.

While trying to defragment the HDD, it stops when it reaches 83% on analysis. I tried to control the volume for errors (including looking for damaged sectors), but that also got stuck at one point.

Edit: I have had a lot of power outages lately, which probably has something to do with why the SSD wouldn't boot.

First thought, do you have the SSD connected to a SATA III port on the motherboard and using a SATA III certified data cable?

Second, I would do another clean install, after "first thought" items, without the other drive connected. Sounds like a possible corrupt install.

There is something "funny" going on between the hard drive and the SSD and possibly the SATA controller on the motherboard.
You stated you couldn't install Windows on the SSD until the hard drive was connected. That suggests something going on with the SATA controller on ports on the motherboard. Did you try resetting the BIOS to its defaults (even if it was at default)?
Did you try moving the SSD to a different SATA III port?

Now that you have Windows installed, you say the hard drive(s) are causing long Windows boot up. That too could be related to the motherboard/BIOS.

Thread starter mentions power outages; not having an UPS in place can lead to hardware problems due to power off, then power on, then power off, then power on -- can cause both hardware damage and damage to Windows operations.

fireberd said:

There is something "funny" going on between the hard drive and the SSD and possibly the SATA controller on the motherboard.
You stated you couldn't install Windows on the SSD until the hard drive was connected. That suggests something going on with the SATA controller on ports on the motherboard. Did you try resetting the BIOS to its defaults (even if it was at default)?
Did you try moving the SSD to a different SATA III port?

Now that you have Windows installed, you say the hard drive(s) are causing long Windows boot up. That too could be related to the motherboard/BIOS.

You misread my post. It says I had to remove the HDD to install Windows.
I can try resetting the bios.
The HDD and SSD are using the only SATA III ports I have, and I could try to swap them, but it's kind of cramped in my case because I actually have 1 cd-rom, 4x HDDs and 1x SSD.

Edit: I reset my BIOS. It said BOOTMGR is missing when I restarted my computer. I inserted my Windows 7 installation DVD, and chose to replace the windows version already installed. I did not get an error about my HDD this time. I'll make another edit when the installation is finished.