You've cloned it incorrectly then, but I've never used that program. I have used several though and had problems with many not working.
You can also try the free version of Acronis True Image from the WD web site (hard drive support and download section). There are two options with that program:
1) CLONE, or
2) Backup/Restore
Try the CLONE option first and if that doesn't work you can try Backup/Restore but you'd need a third drive, or partition the WD drive into two (backup to 2nd partition then restore the backup to the 1st partition).
Other:
I've used Macrium Reflect Free as well but it failed me this time. No idea why, though this time I had Windows 8 installed in SECURE mode (non-Legacy). I cloned with the full version of Acronis True Image and it worked fine (though the instructions are slightly confusing).