In case anyone else runs into the same thing, here's what happened. The Ubuntu installer shrunk the Windows partition and set up /boot/grub/menu.lst to dual boot, which is all good except that it made a mistake and put
title Windows Vista/Longhorn (loader) root (hd0,0) where it should have put (hd0,1). The installer assumes that the first partition on the drive has Windows, but on this system the first partition has stuff to reinstall or repair Vista. This makes it look like Ubuntu hosed the Vista installation, which I'm pretty sure isn't the case. I'm not entirely sure because in my confusion I ended up reinstalling Vista. Anyway, next time I do this I'll try editing /boot/grub/menu.lst first.
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