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();
The error is coming from an incorrectly protect call to annotationPanelisVisible(). in the isAnnotationUtilityPaneVisible() method. Once this it is properly protected the viewer loads.
I think the likely cause was that the annotation was set into invisible via the properties which get the swingController in the state that causes the null pointer.