New internal hard drive replacement not seen - why?

I have replaced the internal Seagate Momentus 7200RPM, 160Gb drive on my 2007, 17 inch MBP- with a Seagate Momentus 7200RPM 500 GB. I used Super Duper to clone the original drive - and the new drive will boot up OK - BUT only when in an external enclosure! Not as the new internal drive.
I am using Mountain Lion 10.8.2
When it is in place in the MBP at start up I get the flashing Question mark. I have tried booting from another backup drive - to use Disk Utility to repair the new drive. but it does not show up! I have also tried booting from OS Mountain Lion on a flash drive - but, again I cannot 'see' the new Seagate internal drive to repair it!
I have checked all the connections (taken the new drive out and put it back in several times) all connections appear to be Ok.
I have tried resetting PRAM - no difference.
So, why does it only work when connected as an external drive - and does not show up when connected as an internal drive?
PLEASE - can anyone help?
thanks
Alan

Hi again - thanks! I recall the cable snaking around and it certainly does look as in your pic.
As I put in my first post - I do have an enclosure and it does work from that. However, it is only via USB 2 so is slow. As I write I have booted up from my Firewire 800 backup drive.
I will explore bot iFixit and Powerbook medic and see if they can send these parts to me - so thanks to you both for all this helpful advice!
One final question - since it WAS working when I first took out the original drive it may be that I have EITHER pulled too hard and broken a connector - or just pulled one loose
Is ther any way I can test? How are the other ends connected? The large block of double connectors to the drive is clear - but I have not tried specifically to remove any other ends!

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