I have disabled Preferences -> User interface -> Status window -> "Show status window" and the window is correctly not shown. But when I (re)start KDE the window is shown (again) and the option in the preferences is also activated too.

When I play around with the checkbox the window gets correctly shown or hidden depending on the setting.

I also tried manually Quit-ing workrave before shutting down KDE (thinking it might have something to do with workrave not exiting correctly and not saving its settings correctly) but this produced the same result as just having workrave being stopped automatically during KDE shutdown.