2010 13" MBP Wont boot from internal. Will boot from external

This is fairly long winded, I will try to be as clear as i can.
Last week my 13" MBP refused to boot after running out of battery during sleep.
I have done the following to the original drive:
Booted from Lion Recovery, repaired, verified, and repaired/verified permissions.
Booted from Snow Leopard DVD, done the above.
Used Disk Utility on another Mac, done the above.
The drive still will not boot from the internal cable.
I can see the drive when attached internally, but cannot do any of the above actions as it is "unable to unmount"
I can boot from the drive if I use a USB external adaptor.
I bought a new hard drive....
I have done all the same on the new HDD with additionaly installing fresh Lion / Snow Leopard to the new drive whilst its in the internal position (Leopard from the DVD originating with my laptop, Lion from Lion Recovery whilst the other drive was on USB) but still having the same problem when it comes to booting - i.e. wont boot from internal. will boot from external USB.
Ideally I would like to end up with a lean install of lion, on the new hdd, booting from inside the laptop.
Please help, this is driving me mad.

I think you have solved your own problem. If you have two different HD's and they both do not work once connected, but do when placed in an external enclosure, then I would think it has something to do with the connection.
Slap the old drive back in the machine, and take it to the genius bar, and have them diagnose it. Hopefully they will have an answer for you. If not, bring the other drive too inside he external enclosure, and show them that it boots via the external.
Then, lay the whammy on them, and tell them that the original drive works inside the enclosure too.
Would be interesting to know what the actual issue is, and the resolution as well...

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