MacBook Pro doesn't recognise new Internal HDD

Hi there, I was hoping to get some help on this ...
I purchased a WD Scorpio Blue 750GB internal HDD and Apricorn kit and used SuperDuper to clone my current internal HDD. The clone copy worked fine and I can boot the OS via the new WD HDD if it’s connected via USB, but when I install it inside, the Macbook doesn’t recognise it and a folder with a blinking ‘?’ appears.
I’ve tried booting up from the disk utility on start up to hopefully select it and that doesn’t work either as it cannot find the HDD.
I’ve tried booting up from disk utility and using my Time Machine back-ups to copy over the new WD HDD but it doesn’t recognise the new internal HDD either.
I did format it before I cloned the new drive to be OS Extended (Journaled) but I didn’t make multiple partitions and not sure if this is a step I'm missing.
When I put the old HDD back in it boots fine.
Any advice would be greatly appreciated
Cheers, Sam

Didn't matter how many times I reformatted, partitioned mapped the HDD when it was connected externally, the issue was was the Super Duper clone. (even though it would start up as an external start up disk.)
Had to install the new HDD internally and reformat it from boot up through Disk Utility then do a restore from a previous Time Machine back up.
Works fine now, no issues.

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