Bootcamp 3 adds support for mounting your Mac's HFS partitions. By default, Windows Update tries to use the hard drive with the most free space during installs. For many users, this may well be one of your Mac HFS volumes.
The way to resolve this is to unmount the Mac volumes first, leaving Windows Update only Windows-formatted volumes for use. I used XP's built-in command line program Mountvol to unmount the Mac partition. After that, running the updates was smooth sailing.
Warning: I am not explaining here how to use the system Mountvol to unmount volumes, as if you get this wrong, there is a good chance you could loose data.
[robg adds: I can't test this one yet, as I don't have Boot Camp installed on my 10.6 machines. However, I would think the contextual menu in Windows should allow ejecting non-system volumes, but perhaps that's not the case.]
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