Public bug reported:

Below is the original text of the question as I posted it. Underneath some new 
information.
Thanks
Oliver Kluge

Hi,

I want to install Ubuntu 10.04 LTS Desktop AMD64 on a PC that has a
terabyte sized hard disk, which is already fully partitioned (with two
partitions prepared for Ubuntu and Ubuntu's swap device). On that system
there is a Logical Volume Manager installed (IBM). This LVM could be
ignored by Ubuntu, as it is meant for an existing, working, bootable JFS
partition containing eComStation, which is the current version of IBMs
OS/2.

But unfortunately, Ubuntu trashes the LVMs information on the disk,
either the DLAT or the BBR. After installing Ubuntu _and telling it not
to install Grub2 into the MBR (!)_ the LVM info gets damaged beyond
repair. Ubuntu runs flawlessly, having actually installed Grub2 into
it's partitions PBR, as instructed.

But eComStation won't run, and a Logical Volume Manager run from CD
complains corrupt partition info (the actual partition table is intact.
But disk editing tools like DFsee show that it's the LVM info that got
damaged).

IBMs LVM stores its info in the last sector of track 0, as opposed to
the MBR which of course is in the first. The MBR is not damaged. It
boots IBMs boot manager out of a small partition, and that runs okay. It
will boot Ubuntu and every Windows installed on the system, but because
of the damaged DLAT and/or BBR no longer eComStation.

The error can be pinned down to Ubuntu. Immediately before installation
everything is fine, immediately afterwards it is broken, reproducibly.

Anyone got a hint why Ubuntu does this, even when told not to install
boot code into /dev/sda?

Thanks
Oliver

New information:
a) Happens with 10.04.1, too, and also happens using the installation function 
of a running Live Ubuntu
b) I bulk copied the entire hard disk to external storage and so I am able to 
binary compare immediately before and immediately after installing Ubuntu in 
/dev/sda9 (and Grub2 in there, too, not into the MBR). I am scanning the whole 
disk, but apparently Ubuntus installer wrote, without permission, into 
/dev/sda5 which contains the JFS partition of eComStation.

Thanks
Oliver Kluge

** Affects: ubuntu
     Importance: Undecided
         Status: New

** Bug watch added: bugs.ecomstation.nl/ #2914
   http://bugs.ecomstation.nl/view.php?id=2914

-- 
Ubuntu installation writes into foreign partitions
https://bugs.launchpad.net/bugs/669459
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