Here is my setup
I had to reinstall windows because of obivious windows issues. After the install I could not boot ubuntu. I tried a few from this posts but none of them worked for me. Finaly It worked when I used the following method.
1. Boot live cd of ubuntu (I used xubuntu)
2. Ran Gnome Partition editor
3. Changed the boot flag from windows partition to the linux partition
(I ran those grub root and setup commands to my linux partition before I changed the boot flag so I don't know if those commands had anything to do with it or not)
Hope it helps to some like me.