Slow Harddrive is Dragging the System

First thing I would check is the Hard Drive's health. (NOTE: if you have a bad drive defragmenting it before checking the SMART status can essentially shred your data). Go to http://www.smartmontools.org/ and download the windows version. Then open a CMD prompt and check the SMART status.

C:\Program Files\smartmontools\bin\

smartctl -a /dev/sda/

If you see a poor health status - you found your issue. Replace the drive.

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If the status is good:

Move on to other troubleshooting. Since Ubuntu and Windows are experiencing the issue - drivers are not at fault. Check the BIOS for AHCI mode - yes you can change this after the OS is installed. If the drive is in IDE mode things will crawl regardless of drivers installed.

You will find the setting under Advanced in the BIOS computer setup menu.