WorkingHours did undergo a big rework that changed how certain features work.
Dimitri What does "logging out" refer to in the options?

Again: Does the timer start as expected when you log in to Windows? You have set it to "Start/resume timer":

Please also update to the latest version 2.15.1 - most likely it won't make a difference, but just to be sure...
Also, do you see any WorkingHours-related crash reports in the Windows Event viewer program under "Windows Logs" -> "Applications"?
Also, is the WorkingHours app window running when you shut down? If WorkingHours is not running, it does not receive the shutdown event