On my main machine (NOT the vbox test described above) I have this kind
of setup:
 Device Boot      Start         End      Blocks   Id  System
/dev/sda1               1        2550    20482843+  c7  Syrinx
/dev/sda2            2551        6375    30720000    7  HPFS/NTFS
/dev/sda3            6376       36746   243955057+   7  HPFS/NTFS
/dev/sda4   *       36747       38913    17406427+   5  Extended
> /dev/sda5         36747       38378    13109008+  83  Linux
> /dev/sda6         38379       38913     4297356   82  Linux swap / Solaris

sda1 & sda2 are windows, sda3 is storage.

sda4 is the "extended" partition "containing" sda5 (ubu 9.04) and sda6
(swap)
For various reasons I have the first 512b part of grub installed to sda4
("root (0,4); setup (hd0,3)"), which is being chainloaded.
When installing ubuntu to a usb stick (not liveusb) these 512b of
bootloader were wiped and ubuntu is unable to boot.

Attached logs from the installer


** Attachment added: "partman"
   http://launchpadlibrarian.net/34294490/partman

** Attachment added: "syslog"
   http://launchpadlibrarian.net/34294491/syslog

** Attachment added: "version"
   http://launchpadlibrarian.net/34294492/version

-- 
ubiquity overwrites VBR of extended partition
https://bugs.launchpad.net/bugs/445067
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