This is for older computer systems surely? this is why computer management was invented for the new windows systems. Also Fdisk is not recognised at the command prompt.
The instructions on the Microsoft website say to create a boot diskette and run fdisk from there. You would not want to repartition an actively-used HDD, which may be why you can't get to fdisk from the command prompt.
If it were me doing the job, I'd boot a live Linux CD and use the Linux fdisk to toggle the flag, since I know it can easily do the job. You would just open fdisk from the terminal and hit "a" to mark a partition as bootable. I have not used any Windows beyond XP extensively, so if there's something new in the management console in Vista or 7, I am probably not aware of it.