With the manual method of useing the Bootrec commands while booted you can build a fresh BCD store on a drive that was unbootable to start with. That was gone over last year when custom installing a second RC install and later wanting it to be stand alone while the host drive saw everything there.
When seeing the 7 mbr trashed by Grub when custom installing a distro onto a flash drive the startup repair tool "failed after several attempts" to get 7 running again. One trip to the command prompt option to rebuild the BCD store and the use of the two Fix commands(Fixboot, Fixmbr) was the solution.
Sometimes the only thing that will work is a manual repair ta a command prompt despite the bonus of having seen the startup repair option made available in both Vista and 7.
A repair install for the most part replaces to refresh the main system files not so much geared to repair the boot sector. That's mainly due to already being booted into Windows when starting the OS repair. You are not seeing a fresh custom install which is a full install where the boot files and information are then added fresh.