Cannot see internal HD

I was working on my Mac when it froze, waited few minutes only had the revolving circle icon, hence powered off by holding down power button. When i restarted it showed me the ? in a folder. Rebooted holding CMD+R, ran a disk utility stated disk which saw the HD and ran a test and confirmed ok. I then tried reinstall OSX but the system couldn't see the HD disk to continue? Real strange.

I then took the HD out of the unit mounted in an external case and connected to another MAC - I could immediately see my folders, everything, so copied across most important files then took the disk back to the original MAC it came out of but this time connected it via the USB port to the original Mac (which now had no internal disk of course) and rebooted using CMD+R. Again ran disk utility no problems, then ran reinstall OSX and could see the HD connected via the USB, so did a complete reinstall OSX that way - on completion everything tested out ok and rebooted Mac several times with HD connected via USB and ran perfectly proving I feel that somehow the partition info had screwed up.

Reinserted the disk (now proven again) back into the Mac and rebooted - ? in folder comes up and again if reboot using CMD+R can run disk utility says ok, but fails to see disk if run reinstall OSX..

HELP what am I doing wrong....