I could not reproduce is as default behaviour.  I did in Gutsy:

    kdesu konsole

and no knemo instance shows up.    What are you doing to
trigger the second knemo instance?

FWIW:
knemo is a implemented via a kded service.    Every KDE
application needs a kded running.   So
when you run an kde app in the login environment of
another user, a second kded is started for the user and
therefore a second knemo is run.

With this in mind I can reproduce you problem with some handish work:

       kdesu konsole

then as root in this window

HOME=/root
cp ~<myuser>/.Xauthority  ~/
kwrite &
ps -ef | grep kded

now a another kded is listed and therefore another knemo.
Why this happens by default is not clear.

Please give a concrete example that triggers the second knemo.

Can you run:  kdesu konsole

  o is another knemo running?
  o is there a new kded process (ps -ef | grep kded)
  o what the output of
     printenv $HOME
     printenv $KDEHOME
    when you run in in the kdesu konsole window

Achim

-- 
two knemo icons while running anything with kdesu
https://bugs.launchpad.net/bugs/159810
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