New HDD Will Not Boot Internally

I'm trying to install a 1TB HDD into my MBP in place of the 750GB that came with it. I wouldn't have thought this to be important information, but this 1TB drive has come from inside a Seagate Expansion. I've cloned the drive, and made sure it will boot externally, but it will not boot when internal! Here are all the things I've done to try and make this work:
With the Expansion unit still as sold, I connected externally and formatted the drive to Mac OS Extended (Journaled). With the old 750GB drive still internally, I booted into Recovery Mode and used Disk Utility's "Restore" function to clone the 750GB drive to the 1TB. Once this was done I used the Startup Manager to boot from the newly cloned 1TB drive. This worked fine!
Taking the old drive out, and putting the new one in, I used the Startup Manager to select the new drive and it wouldn't boot. It came up with the Apple screen and spinning wheel, but wouldn't get further than that.
Thinking that some boot information hadn't been copied, I attached my old drive externally so that whatever information wasn't copied was at least accessible, but the new drive still wouldn't boot.
I took the new drive out and connected it externally via USB again, but this time with no drive internally. I selected the new drive in Startup Manager, and I was able to boot from it.
Unsure of what's going on, I wiped the new drive and put it back in the MBP. Booted into Recovery Mode and selected Restore from Time Machine backup. I went through the selection of where my backup was and which one to use, but my new 1TB drive wasn't available to restore to.
I then tried the option to Reinstall Mac OS X, however it wouldn't let me do this either.
I went to Disk Utility in Recovery Mode, with the new drive still internal, to see if the disk needed repairing. I noticed then that it didn't appear to have the same name I'd given the partition when I'd formatted it, and I was also unable to reformat it, erase it, or actually do anything to it at all.
For whatever reason, this hard drive will NOT work when installed internally. I've contacted Seagate and they basically told me to shove off for opening the unit and voiding the warranty, no one online seems to have any ideas as to why this isn't working!
If anyone has some great ideas for a solution they'd be more than welcome!

It worked! Drive and Recovery Partition were cloned without problem and I can now boot to the internal drive as normal.
Thanks for the help Grant!
The fix/method for anyone wanting to do this in future:
Install new HDD into Mac, connect old drive in an enclosure.
Boot to old drive recovery partition
Run Disk Utility from the recovery partition and 'restore' the image of your old drive (which is connected via USB) to the new drive.
Wait a LONG time (5 hours for a 750GB HDD) and it'll clone your entire HDD including the recovery partition.
Whilst still in recovery Disk Utility, change startup disk to the new HDD (the one installed in your Mac)
Disconnect USB drive and boot to the newly cloned intertnal drive.
Celebrate - up to you how to approach this one, I just did a little dance.

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