I have this problem too. Ubuntu Edgy. 
Don't know if it is relevant, but if I start k3b from a terminal I get this 
message when I try to update the permissions in the setup:

qstring_to_xtp result code -2
Session management error: Authentication Rejected, reason : None of the 
authentication protocols specified are supported and host-based authentication 
failed

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k3bsetup fails to change permissions of programs
https://launchpad.net/bugs/54264

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