How can I tell Win2k (or more specifically, its on-boot filesystem checker), to ignore the existance of a hard-drive (the disk in question contains my Linux install, and scandisk stops to check it every boot, when I don't want it to even touch it).

I had the same problems... Linux on the primary Master, Windows on the primary slave, and it slowed to a crawl... Other versions of Windows does not do this, only 2K?

Anyway, I simply disabled it in the Device manager.

Cured the problem straight away, and this worked on 4 systems that were dual booting, so I seriously doubt you need to do all that stuff in the registry!