If you don't use hibernation right, partitions can go missing. I learned this the hard way with 250GB of "precious data" loss.
"can't write $MFT". if you see that, the OS couldn't write your filesystem and your filesystem is now hosed. typically this happens when you were in hibernation, had a drive connected before and then disconnected it or powered it off when booting the next time out of hibernation. learned this from experience. :-(
I tried stellar phoenix (NTFS recovery software) - it didn't see a thing. I tried testdisk. it didn't see a thing. Thoroughly hosed. but photorec was able to recover some files, though it did a terrible job with filenames (all numbers - totally useless)! so hosed.
IN OTHER WORDS:
hibernation likes to keep the same peripherals/drives powered up during boot as things were when it was shut down, or else there will be trouble. you only lose the hibernation session if you power up a new device (I don't know about windows vista/7).
WHAT YOU CAN DO IF THIS HAPPENS
You can try a data recovery shop to see if you can get your data back, but it can cost $250-$1000 I hear. no guarantee of results folks. the names are gone!