What is the problem?
Since Plasma 5 was released, systray icons needed to be updated if they used the xembed system - more on that here: http://blog.martin-graesslin.com/blog/2014/06/where-are-my-systray-icons/. Some apps haven't yet been updated (bug report was raised here https://issues.workrave.org/show_bug.cgi?id=1211 but hasn't yet been acted on) which renders the system tray items unusable.
How do we fix this?
While the actual bug hasn't been resolved, thanks to Minio from the KDE forums, there is a simple script for KDE which allows you to access the settings and preferences here - https://forum.kde.org/viewtopic.php?f=22&t=107181 - even though it was written years ago, it still works! Simply create a script and run it to gain access to your Workrave settings.