Dreaded Question Mark... But with a Catch!

The other night my mid 2009 MBP froze. I got the pinwheel and it was unresponsive. I gave it 10 minutes to come to, but it never did. I held the power button to turn it off, and then turned it back on. After a couple of minutes of blank white screen, I got the blinking question mark/folder. After searching the forums, I tried everything. CMD+R, the option key, etc. Nothing worked. The biiiig problem was that my last TM backup was corrupted, and I couldn't be bothered to spend the time doing a fresh backup. Well I pulled my HD, put it in an external enclosure and booted from it. Guess what? It worked perfectly. I was able to do a fresh TM backup, and used the computer this way to surf the internet today. I thought maybe it was some kind of fluke and put the HD back in my MBP. I checked the sata cable where it meets the motherboard, and it was fine. I booted it up, and I'm back to the question mark. Why would my HD work as an external, but not as an internal?