I had the same problem what are we to do with "Vista"? I ran "repair, restore, and to the store". I thought what did I do? Everything was just fine this is the second time that this has happened and the last I lost almost a full "tera" as I had to reinstall all.
This time I wasn't giving up so easy, CHECK YOUR BIOS!!!!!
CHECK YOUR BIOS
That is what I did and I found that someone "thing" *(Vista)*?? had installed a virtual drive as a start-up drive in place of my "tera". Not sure what it even was called just a bunch of &()*JKJO&*JIJKJ&)((**&()&^%$%$ as a new HDD...
Changed and then fine in next start up.
Hope this helps, and it took me a week to reinstall everything, that was a bitsh....