Sometimes KWin_x11 crashes and then restarts.  When it restarts it forgets the activity settings of all the windows causing them to be displayed across all activities instead of the activities that they were originally relegated to.

One way to work-around this is to open the Window Rules configuration and then save it again.  This does not, however, fix windows that do not have explicit Window Rules, it only corrects the window activity settings for windows that have an explicit window activity rule.

This looks like a regression.