I just fixed a computer with this similar problem.
What I had to to was first run the the repair disk and install the original boot loader. Use a repair disk that corresponds to the operating system installed on the computer, ie., XP, Vista, or 7. To boot using the CD/DVD, make sure in your BIOS boot order, CD/DVD drive is listed as one of the options. Make sure you have the CD/DVD in the drive.
After you successfully boot into the disk, make your way to the "repair" section. What you are going to want to find is an option that says something like "fix startup." Run it, and reboot.
With any luck, provided its similar to my problem, you will be able to boot into windows. There was however another step to my repair, the partitions were not labeled with the correct drive letter path. You will be able to tell that this is the case if;
-After windows loads, you will be at a blank screen with only a mouse cursor in the center.
-"Loading your desktop" or "Preparing your desktop" loading screens are abnormally long.
If this is the case, you are still able to use Ctrl+Alt+ Del. Press these down. Start task manager. When in the Task Manager, navigate to the processes tab. At the bottom of this window, there will be a "new task" button. Type "cmd.exe" (exclude the quotations). A black box should appear. in this box, type "regedit32.exe" (again, quotations).
A new window will appear. From here, use the left navigation to find ;
HKEY_LOCAL_MACHINE\SYSTEM\MountedDevices
Now find the drive letter you want to change to (new). Look for "\DosDevices\C:".
Right-click \DosDevices\C:, and then click Rename. To change the letter, simply type a different letter in place of "C" . (NOTE- You are going to want to change the drive letter to a letter currently not being used by any drive. Try drive letter "v", so you can shuffle the drives around.)
For example. If I have Drive W and Drive K. If I want to switch these letters, I have to first change one of them, lets say Drive W, to some other letter that is not K. Ill change it to Drive P. This now frees up the letter W. I can now rename Drive K to Drive W. Now the letter K is free. I now rename Drive P to Drive K. I now have switched the original Drive W to Drive K, and the original Drive K to Drive W. Drive letter "P", was only used to free up letters W and K.
In my case, my boot partition and my regular partition were switched, as in, my E drive should have been my C drive, and vise versa. So if this is the case for you, you most likely will have a C drive and some other letter. Your C partition should be your regular data partition (this will be the larger of the two). The smaller partition should be the other letter (whichever your system uses), and this should be your boot partition.
This is what fixed my clients problem. I hope this helps.
