Macbook Pro boots successfully when using hard drive in USB enclosure but doesn't boot when connected internally

Macbook Pro boots successfully when using hard drive in USB enclosure but
doesn't boot when connected internally

Apologies for the long question. I will keep it as simple as I can.
Last week my Macbook Pro (13-inch, Mid 2010) started to act strange.
It started when I tried to open Skype and received an error complaining
that the program could not start because Skype could not read (or lock,
unfortunately I can't remember) it's skype.plist file.
I restarted my Macbook hoping that would fix the problem (and I hadn't
restarted in a while so I figured it was overdue).
My Macbook restarted and played the startup chime but then hung at the
grey startup screen with the spinning wheel. I thought nothing of it and
did a hard shutdown but no matter how many times I did, the Macbook never
advanced past the grey startup screen.
I tried to boot using Safe and Verbose mode and got the following error in
both cases:
BootCacheControl : Unable to open /var/db/BootCache.playlist: 22 invalid
argument
I googled the error and tried various solutions with no luck.
The Macbook would boot to the built-in Mountain Lion recovery partition.
At this point I decided to backup my data so I could mess with the hard
drive a bit more without fear of losing any data. I booted in to the
recovery partition and cloned my hard drive onto another using a USB
enclosure. It seemed to work OK and I verified all of my files were on the
backup hard drive by plugging it into another Macbook.
After cloning my hard drive I verified and repaired the disk and disk
permissions using the disk utility in the recovery partition but that had
no effect.
At this point I decided to reinstall Mountain Lion. I tried numerous times
to reinstall it with the hard drive inside the Macbook (both using the
recovery partition and a bootable Mountain Lion SD card) but couldn't get
it to install. Eventually I got it to install, but only when the hard
drive was placed in a USB enclosure. I knew this probably indicated a
bigger underlying problem but decided to go ahead anyway.
I installed Mountain Lion successfully but now it will not boot with the
hard drive connected inside the Macbook, only when it is used in my USB
enclosure. When the hard drive is placed in my USB enclosure it boots to
Mountain Lion without any problem.
With the hard drive inside the Macbook:
If the Macbook is booted as standard, it hangs on the grey startup screen
with spinning wheel
If it is booted in verbose mode, it seems to boot successfully (shows no
errors when the white text show up) and then hangs on a black screen with
a solid white cursor in the top left corner (I can type at this point but
it does nothing, it doesn't appear to be a terminal window)
If it is booted in safe mode, the progress bar appears, progresses to the
end and then hangs on the grey startup screen with spinning wheel
I noticed a lot of suggestions on the internet to replace the hard drive
cable to the motherboard. I did and it had no effect.
I've tried using another hard drive running a brand new install of
Mountain Lion and that behaves exactly the same (boots fine using a USB
enclosure but doesn't boot when connected internally).
I've booked an appointment at the Apple store but figured it was worth
posting the question anyway, in case anybody has a similar issue in the
future (hopefully I'll be able to post the answer, if nobody else does,
after a visit to the Genius bar).
Any suggestions?
Thanks for reading.