Configuration:
* My user is an administrator on the local computer.
* I only have the sys tray icon showing, no status window, no applet.
* Not sure it matters but I am connected to a domain.

Problem:
If I mistakenly left-click on the tray icon the status window opens. After this it doesn't matter if I close the window or if I use preferences to turn it off again, the "show status window at startup" flag has been set and is stuck.
From then on, at every restart it starts with the status window open.  

Work-Around:
The only way to get it turned off is to quit workrave, right-click on it and select "run as administrator".  Then I can change the preferences, hide the status window, and the settings are saved correctly.

Observation:
It looks from the outside like:
* The code that executes on "left-click the sys tray icon" is able to change the preferences and save them when running in the normal mode.
* The code that saves changes in the preferences window cannot save changes in normal mode, it must be in the "run as administrator" mode.

I cannot reproduce this with the latest snapshot (http://snapshots.workrave.org/20111022/workrave-win32-v1_9_900-4-g20b4efeafa-20111022-installer.exe)

Workrave stores all of its settings in the registry. Could you please check with regedit.exe if the 'enabled' value of the key 'HKEY_CURRENT_USER\Software\Workrave\gui\main_window' changes if you toggle the setting 'User Interface -> Status Window -> Show Status Window'.

Thanks.

Doubting my sanity here. I cannot reproduce the issue now... I haven't update workrave. I have received Win 7 updates...
Whatever, something resolved it.
Sigh

No problem. closing bug report. please reopen if the problem resurfaces.