The Global file site.rmg and its definition in the locations will override some not properly documented values from the dtabase with local values on the workstation and if used can cause problems if the user is not aware of the situation and the details. In order to use the valaues from database only the file site.rmg must not exist on the workstation and and the definition must be blank.
That is the way I like, because then I get what I expect to get.
Sorry to say that did not provide explanation to your experience.
Consider resintalling OWB, schedule connect and jre. After uninstall clear the registry for Open Workbench and Niku entries before reinstall.
Which versions of Windows, Windows bits, Clarity, OWB, schedule connect and jre are you using?
Martti K.