Bug 334644 Cannot manually un/render a window that's directly under the application
Setting the 'toBeRendered' flag for a window that's a direct child of an application does nothing. The workaround is to manually de/construct it via the IPresentationEngine.
bundles/org.eclipse.e4.ui.workbench.swt/src/org/eclipse/e4/ui/internal/workbench/swt/PartRenderingEngine.java
Shell limbo = getLimboShell();
				runContext.set("limbo", limbo);
				
				
				
				testShell = null;
				theApp = null;
				boolean spinOnce = true;
				if (uiRoot instanceof MApplication) {
					ShellActivationListener shellDialogListener = new ShellActivationListener(
							(MApplication) uiRoot);
					display.addFilter(SWT.Activate, shellDialogListener);
					display.addFilter(SWT.Deactivate, shellDialogListener);
					spinOnce = false; 
					theApp = (MApplication) uiRoot;
					
					MWindow selected = theApp.getSelectedElement();
					if (selected == null) {
						for (MWindow window : theApp.getChildren()) {
							createGui(window);
						}
					} else {
						
						createGui(selected);
						for (MWindow window : theApp.getChildren()) {
							if (selected != window) {
								createGui(window);
							}
						}
					}