Comment 3 for bug 517121

This is definitely a problem with the Fujitsu-Siemens Amilo Si 3655. It seems like the bios (Phoenix, latest version 1.03c of 2008-09-22) in this machine refuses to execute the MBR boot code if the first sector in the active primary partition is blank. And I believe this will always be the case in a common Ubuntu or Debian install.

The grub-installer package seems to be the culprit here, and /usr/bin/grub-installer explains it all:

  # Make sure that there's *some* active partition; some BIOSes
  # reportedly don't like it otherwise.

and if no sensible partition is found for the task:

  # We don't care at this point; just pick the first
  # primary partition that exists.

A workaround would be to switch to console 2 (Alt-F2) and do a 'fdisk /dev/sda' with the five commands 'p-a-2-p-w' (replace '2' with the partition that shows up having the 'Boot' flag set), and then back to the install console with Alt-F1. This can be done just before rebooting (and after configuring grub-pc).