I can't boot from new hard drive when it's installed in my Macbook Pro.

I used Carbon Copy Cloner to make a copy of a drive on it's way out. I can boot from and use the new drive normally when it's connected externally, but when it's installed in my Macbook, it refuses to find it and shows the blinking folder with question mark on startup. Also I can't open Disk Utility or any of the key command boot modes when it's internally installed. When I ran the drive through Disk Utility while it was externally mounted, it said the partition was fine but when I tried to diagnose the actual drive it said "Alert: Unrecognized file system." Any help would be appreciated!