HP ProOne 600 G1 AiO will not boot with WD My Book 1140 3TB USB Device Plugged In

When I have the WD My Book 1140 USB Device plugged in and reboot the computer, It won't boot.

From my hand written notes:

Windows Failed To Start

File:\windows\system\config\system

Status 0xc00000e9

Windows failed to load because the system registry file is missing or corrupt.

I have tried  the following:

• making sure the SATA drive is 1st in bios boot sequence.
• Disabeling legacy support in bios for this USB drive
• removing  the drive from the bios boot menu

What else can I try to resolve this?

Also, after I unplug the device and reboot I am presented with the standard Windows 7 menu asking me if I want to run start up repair or start normally. Once I made the mistake of selecting start up repair which made the system completely un bootable and I had to restore the drive from a current shadowprotect backup that is on the WD Mybook. Why would startup repair wipe out my hard drive?

Also, I found these on the subject by google:

http://answers.microsoft.com/en-us/windows/forum/windows_7-hardware/7-wont-boot-with-external-western-digital/0f35b59c-f383-45f7-a95e-c238676e0880?page=1

http://wdc.custhelp.com/app/answers/detail/a_id/3701/p/228%2C209%2C316/c/130/session/L3RpbWUvMTM3NzU2NDI5MC9zaWQvOUdCeFRNeWw%3D