Internal Hard Drive not showing up

I used an iFixit kit and great instructions to replace the CD drive with a SSD a couple of years ago in my son's laptop and it has been working fine. I don't know if it became overheated, electrocuted or what but when he came back from school the whole system was near death - can supply further info. if needed, but 'near death' sums it up.

I managed to wipe and rebuild the SSD and get that back working properly but the internal HD (500Gb) just wouldn't show up. The MBP works fine without it, quite quick in fact as the OSX is on the SSD.

I took the HD out and put it in an external enclosure, got it to appear, reformatted it etc. and that now seems to work fine as well on its own. But not when it's back in the MBP. I can hear it spinning up so it's getting power, but it still won't appear as a volume on the desktop, in the System Report or in any diagnostic utility.

All the ribbon connections seem fine and there are no other problems. Where do you think the fault lies? and is it worth fixing, now it's out of Applecare period?