I have 2 hard drives on my machine, one with BT4 and the other was empty, until recently decided to put windows on it, so, I unplugged the first hard drive (the one with BT4 on it) and set the empty drive as the first HDD, after successfully installing and booting windows on the empty drive, I plugged in the BT4 HDD (as the first HDD now) and got the error 'Error Loading Operating System'.
I tried booting into an ubuntu live CD (just one I had on hand) and can see all the files on the filesystem for backtrack (Except the files in root?)

I'm not sure what to do? Any advice?