I have the same issue since kde 4.8, and it persists even after today's update to kde 4.9.5. It also has some other side effects, such as global shortcuts not working and the language icon disappearing. In my case it happens randomly, roughly 1 out of 5 times. According to my observations, it seems possible that it happens only when the klipper is the first system tray icon to load.
It's only a minor inconvenience, I simply reboot when that happens. But I've been wandering - is it a KDE issue? A PCLOS issue? Or is it because I haven't changed my user settings since 4.5? (no, I'm not recreating them from scratch just to test it, this is a *heavily* customised desktop)