MBP 2011 can't find harddrive (not problem with drive or cable)

My early 2011 MBP 13" was running fine, then froze up. On restart I got the image of the folder with a question mark on it (the Mystery Folder) - the system couldn't find a drive to boot from.
I took it to a genius bar and the, ahem, "genius" said the system couldn't find the drive because of a problem with the drive. "The drive's dead" he said. I hadn't backed it up, and was freaking out that I'd lose all my data. The only option he said Apple could do would be to take it away (for a week) and put a new hard drive in for £80. They'd take the old drive out, and I wouldn't get it back to try and recover the data.
I asked about replacing the drive myself, as I've done that on PCs, and he said I could try it.
I bought a new hard drive, and an external enclosure. I put the new hard drive in the MBP - Mystery Folder. I put the old drive in the external enclosure - it starts up! Everything still there, exactly as I left it when it froze. I clone the old hard drive onto the new one, try booting from the new drive in the MBP. Mystery Folder. I connect the new drive with an external enclosure - it starts up! And everything running fine.
It's the cable, I hear you cry. So I ordered a new internal cable. Replaced it. Started it up. Mystery Folder.
So, it's not the hard drive, it's not the cable. What is it?!

Hi Ogelthorpe.
That's right - I now have 2 hard drives, clones of each other.
Both will boot when in an enclosure and connected with a USB.
Neither will boot when inside the MBP.
So it's not the drives that are the problem. Therefore it's an internal cable problem?
I replaced the cable.
Neither drive works when connected internally with the new cable.
What else could it be that means the system can't see the hard drive when connected internally?

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