It also should be noted the the properties manager persists the state of any property in 6.3. On first load org.icepdf.ri.viewer.res.ICEpdfDefault.properties is used. If a customer viewer state is preferred it may be easier to update the properties file instead of directly manipulating the PropertiesManager.
Also the properties Manager can be reset and the next use of the Viewer will restore the defaults.
PropertiesManager properties = PropertiesManager.getInstance();
properties.getPreferences().clear();
Marking as fixed.