Hard drive boots over USB but not when install internally I am trying to upgrade from a 500GB HD (http://www.newegg.com/Product/Product.aspx?Item=N82E16822136314) to a 1TB HD (http://www.newegg.com/Product/Product.aspx?Item=N82E16822152291). The only spec difference (other than capacity) as far as I can tell between the two is that the 1TB HD is SATA 3 (6Gb/s) while the 500GB HD is SATA 2 (3Gb/s).

I installed OSX Lion to the 1TB drive while it was connected to my laptop via a USB to SATA cable. I can then boot from that drive while it is connected via the USB. However, if I install it in the HD bay in the laptop (13" Pro, late 2011) then the screen shows a blinking folder icon with a question mark on it.

Booting a GParted Live USB while the drive is internally mounted (i.e. hooked up directly to the motherboard) shows it as being marked "unallocated" as if there were no partition. However, if I boot into the GParted Live USB while it is hooked up via USB it recognizes the partitions (though it does flag them, saying it can't read them). The 500GB drive shows up whether mounted internally or via USB without any flags.

The common suggested fix is that the internal SATA cable is faulty. However, I am not experiencing any problems with booting from my current HD, so I think that is not the problem. The new HD also seems in good working condition since it boots from USB just fine. My suspicion is that the backwards compatibility from SATA 3 to SATA 2 is not working as it should, but I'm not sure how to force it to work.
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.