Sorry I didn't get to this sooner like I said
When you boot into Ubuntu, on the menu bar, click Places, then Computer. You should see the two harddrives there. Open the secondary harddrive with the good installation and navigate to:
Copy the all the files in this directory (not the folders).
Now open the harddrive with the bad installation on it and navigate to the same location and paste the files.
Then take out the Ubuntu CD and see if you can now boot into Windows.
Humans are the only creatures that won't live up to the their potential. Give everything your all. When you die, die on E.
So I ask you, what do you intend to do now?