I've been using workrave with wmaker for years.  I recently switched to Gnome for short while, during which time I had workrave in the taskbar at the top of the screen.  However, upon moving back to wmaker, when I start workrave, the normal workrave window doesn't appear.  Perhaps it thinks that it doesn't matter as it is still running in the taskbar, except, of course, in wmaker, there is no taskbar.  So I can't see the timings or configure anything, although the popup dialogs still appear every few minutes.

Furthermore, I'd like to point out that moving .workrave to something else doesn't solve the problem. 

Indeed. Fixed.

Workrave stores its configuration in gconf or in an xml file; depending how it was compiled. You could open gconf editor and set apps/workrave/gui/mainwindow to enabled.

Thanks.