Follow-up Comment #1, bug #29002 (project grub):
I did a further test, which I think confirms this to be a grub problem and
not Windows 2000 NTFS corruption of any sort.
I used the Ubuntu Live CD booting into the VM that just had Windows 2000
installed to the front of the HDD. I added smbfs, mounted a share on our Samba
PDC, and used dd to image the Windows boot partition.
Then I rebooted to the Ubuntu installer, and installed Ubuntu 9.10 behind
Windows 2000 as usual.
Upon completion, I tried first booting to Windows 2000, which stalled at the
usual spot.
Then I booted into Linux from the HDD, and restored the dd image of the
Windows 2000 partition. Rebooted.
Windows 2000 again stalls at the usual spot in the boot process.
I have used an Ubuntu Alternate CD and selected Lilo as the boot manager in
place of Grub2. Windows 2000 boots properly when Lilo is the boot manager.
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