- In the system tray a number of entries was missing, custom ones as well as default ones.
- The shutdown option did not work, neither from the application launcher, nor from the taskbar widget.
- Keyboard shortcuts did not work, unless I restarted these manually from System Settings > Shortcuts & Gestures.
From System Settings > Startup & Shutdown > Session Management, under 'At Login' I ticked 'Restore previous session', and rebooted from a terminal:
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$ sudo reboot
At restart I had my system tray entries all back, and the keyboard shortcuts were working as before.
From System Settings > Startup & Shutdown > Session Management, under 'At Login' I ticked anew 'Restore manually saved session', I saved the session from the application launcher, and rebooted -- et voila! it all worked.
You may need to restart one more time, but this it how the problem seems to be solved.
System: LinuxMint 13 LTS + KDE 4.7