Just for the sake of clarity in my case I am not sure if the 'graphical
root' is causing this, although I did use:

kdesu kate .....

every know and then.

-- 
The error message: "The process for the system protocol died unexpectedly" 
triggers many problems, when logged in as graphical root in Kubuntu Dapper
https://launchpad.net/bugs/49950

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