Windows 2000 repair is to boot the 2000 CD, do the repair (unless this is a sata drive, etc.) and then fix 2000. After that you get to repair the XP boot loader.
Frankly I find running 2000 a bit of a pain on today's gear. The rules are arcane and can stress folk today. Let's hope you can run XP and then use VirtualBox to install a 2000 OS in Virtual Box for whatever reason you need that OS for.