I can not boot the affected system because grub does not recognize it,
means that it is not bootable anymore. I do not want to install ubuntu-
desktop and kubuntu-desktop on one system - the menu gets huge and
confusing by installing all standard apps from KDE and GNOME at the same
time.

Atm I work with GNOME because Kubuntu is not bootable anymore (but it
was before), as already mentioned. I attached files from
"/@/var/log/installer/*" from Kubuntu (I hope I got you right with
"affected system"). After installation of the first system I get a
normal "/" folder with all subfolders like "/boot", "/usr", "/var",
"/dev", "/etc", "/home", etc. After installing the second Quantal system
ubiquity moves all that folders from the first system into "@" and
"@home" on its partition. As a result the first system is not bootable
and not even recognized by grub because there is no "initrd.img" in
/boot, because /boot is now a subfolder of "@" which it was not before
installing the second Ubuntu flavor. I really wonder for what purpose
ubiquity does this. I even wonder why ubiquity touches other partitions
outside the actual install partition at all. I always do manual
partitioning in ubiquity and did not set any mountpoints on other
partitions.

Now that I use standard Ubuntu (also on btrfs) which made Kubuntu not
bootable anymore the actual system looks normal - there is no
"@"-folder. The "@" folder is definitely created by ubiquity - it was
not there before installing the second system (standard Ubuntu) -
Kubuntu was perfectly usable.

I tried to move all subfolders in "@" back to root folder, but most
files from "/@/dev" are not moveable, even with root-privileges.

History of what I did:
At first I did the same thing the other way round, means installing Ubuntu in 
/dev/sda6, then Kubuntu to /dev/sda7 - resulting in the same strange moving of 
all files and folders in "/" to "@" - resulting in standard Ubuntu not bootable 
with "@"-folder, not recognized by grub. From KDE I created another USB-stick 
with standard Ubuntu, installed it in /dev/sda6 (the actual system) - and now 
KDE is not bootable because of the "@"-folder. That is the actual situation as 
I mentioned it in the bug report.

I am quite sure, this behaviour is reproducible on any system. Try to
install Ubuntu in one partition, then another install on another
partition on the same hd, both btrfs. It is probably reproducible on a
virtual machine (I will try that now and let you know the result).

** Attachment added: "installer.tar.gz"
   
https://bugs.launchpad.net/ubuntu/+source/ubiquity/+bug/1060893/+attachment/3368642/+files/installer.tar.gz

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https://bugs.launchpad.net/bugs/1060893

Title:
  Ubuntu messes up Kubuntu installation

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