Hard drive boots over USB but not when install internally
Make sure your Mac is off (not just standby) and turn your Mac on like you always do, but hold the Option key at startup until you hear the boot chime. You'll see a bunch of images of HDs in a row, use the arrow keys to select the drive you wish to boot from and then press Enter. Your Mac should now startup using the selected drive this time, but to make it the default drive, go into System Preferences->Startup Disk and then select your drive again. Click Restart to restart your Mac and save the changes.