The problem still continues. 
$ pkill akonadi_control
$ pkill akonadiserver
$ akonadictl start
works, but its only a workaround. I dont see a reason to delete this 
akonadiserverrc:

[%General]
Driver=QMYSQL

[QMYSQL]
Name=akonadi
Host=
Options="UNIX_SOCKET=/tmp/akonadi-mlinux.xgvO7g/mysql.socket"
ServerPath=/usr/sbin/mysqld-akonadi
StartServer=true

[Debug]
Tracer=null

Or is there anything wrong with it? The problem still occurs every some
logins.

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https://bugs.launchpad.net/bugs/1245979

Title:
  After Upgrade to Kubuntu 13.10 akondai fails to register at d-bus
  session, making kde-pim suit unusable

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