Do I have this right, You boot by default into Windows XP which is on your D: drive not Windows 2000 which is on your C: drive?

How is your system configured?As in do you have a RAID system or is your D drive slaved from your C drive?

How does it boot by default to an OS that is on your D drive?

What was the removal program you downloaded?

As to your problem, can you browse manually to to registry and scan it that way?
You could back up Win XP's reg and store it on your WIN 2000 partition and scan it from there.
A crude way would be to disconnect your C drive then try scanning again.
Have you tried scanning from safe mode?

From within WIN XP start msconfig from the run prompt ans select the BOOT.INI tab, what does it say under Default? Also under Operating systems, does all the partition info tie in with the way you think your hard drives are configured? Try this will all your O/S's and check they are saying the same thing.



A bit more info about your setup could be helpful here!