Can't Access Recovery Options on Cloned HDD

Problem in brief
After cloning a laptop HDD to one with the exact same model number, I can successfully boot to windows but cannot run the recovery options (yet they do work on the original drive). Could this be that the software reads something from the HDD to determine it's not the original drive, and am I able to change this thing? If so, what should I look for in the cloning software?

Long Story
I'm working on a slow laptop that conveniently has two HDD bays, both containing hard drives of the same model number. Better yet, the second hard drive was totally empty. After both drives passed the manufactuer's (Seagate's) long tests, I wanted to rule out the possibility that the system HDD wasn't somehow faulty yet still able to pass the tests (perhaps slow, or intermittently sticks etc). This led me to cloning the system HDD to the data one, and boot from it. The cloned drive presented the same slowness problem, and having extensively ruled out malware and various amendable Windows problems, I was ready to try a fresh reinstall of Windows. So I rebooted and attempted to go to the recovery options.... and this is when I hit a hurdle.

After tapping the key to get to the recovery options, the screen goes black (still illuminated), then after about 30 seconds reboots automatically. I switched HDDs and found that the original HDD loads the recovery options correctly. This told me that the second hard drive wasn't a perfect clone.

Additional Info
O/S: Windows Vista 32Bit
Model: HP Pavilion DV7
Cloning Software: Acronis True Image Home 2011 (Full version)
Note: Rather than a direct clone, I used ATIH2011 to 'backup' the drive (rather than each partition separately) and later 'recovered' the backup onto the second HDD. I made sure to check the option to recover the 'disk signature' during that second step.