The only explanation that comes to mind for what you describe above would be a GRUB upgrade that made wrong assumptions about which OS resides on what drive.
In any case, I cannot see how upgrade-system would have caused this, since it's only an APT front-end. -- Upgrade caused dual-boot grub to destroy Win2K disk https://launchpad.net/bugs/62334 -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs
