Bug 127289 [Markers] SystemFilter and group selection state not preserved
We are not preserving the selection state of the system filters or which group is selected.
bundles/org.eclipse.ui.ide/src/org/eclipse/ui/internal/ide/IDEPreferenceInitializer.java
node.putBoolean(IDEInternalPreferences.SAVE_ALL_BEFORE_BUILD, false);
		node.putInt(IDEInternalPreferences.SAVE_INTERVAL, 5); 
		node.putBoolean(IDEInternalPreferences.WELCOME_DIALOG, true);
		node.putBoolean(IDEInternalPreferences.REFRESH_WORKSPACE_ON_STARTUP,
				false);
		node.putBoolean(
				IDEInternalPreferences.EXIT_PROMPT_ON_CLOSE_LAST_WINDOW, true);
		node.put(IDEInternalPreferences.PROJECT_SWITCH_PERSP_MODE,
				IDEInternalPreferences.PSPM_PROMPT);
		node.put(IDEInternalPreferences.OPEN_REQUIRED_PROJECTS,
				IDEInternalPreferences.PSPM_PROMPT);
		
		node.putBoolean(getHelpSeparatorKey("group.main"), true); 
		node.putBoolean(getHelpSeparatorKey("group.assist"), true); 
		node.putBoolean(getHelpSeparatorKey("group.updates"), true); 
		
		node.putBoolean(IDEInternalPreferences.LIMIT_PROBLEMS, true);
		node.putInt(IDEInternalPreferences.PROBLEMS_LIMIT, 100);
		node.put(IDEInternalPreferences.PROBLEMS_GROUPING, "");
		node.putBoolean(IDEInternalPreferences.LIMIT_BOOKMARKS, true);
		node.putInt(IDEInternalPreferences.BOOKMARKS_LIMIT, 100);
		node.putBoolean(IDEInternalPreferences.LIMIT_TASKS, true);
		node.putInt(IDEInternalPreferences.TASKS_LIMIT, 100);
	}
	private String getHelpSeparatorKey(String groupId) {
		return "useSeparator." + IWorkbenchActionConstants.M_HELP + "." + groupId; 
	}
}