Bug 13507 LinkedPositionUI has a reference to SWT.COLOR_RED
LinkedPositionUI(ITextViewer, LinkedPositionManager) - org.eclipse.jdt.internal.ui.text.link.LinkedPositionUI has a reference to SWT.COLOR_RED which will be unreadble if the user sets their background colour to Red. We will be adding a getErrorText colour to JFaceColours in build >20020411. You may want to use that.
org.eclipse.jdt.ui/ui/org/eclipse/jdt/internal/ui/preferences/JavaEditorPreferencePage.java
setDescription(JavaUIMessages.getString("JavaEditorPreferencePage.description")); 
		setPreferenceStore(JavaPlugin.getDefault().getPreferenceStore());
		fOverlayStore= new OverlayPreferenceStore(getPreferenceStore(), fKeys);
	}
	
	public static void initDefaults(IPreferenceStore store) {
		
		Color color;
		Display display= Display.getDefault();
		
		store.setDefault(CompilationUnitEditor.MATCHING_BRACKETS, true);
		color= display.getSystemColor(SWT.COLOR_GRAY);
		PreferenceConverter.setDefault(store, CompilationUnitEditor.MATCHING_BRACKETS_COLOR,  color.getRGB());
		
		store.setDefault(CompilationUnitEditor.CURRENT_LINE, true);
		PreferenceConverter.setDefault(store, CompilationUnitEditor.CURRENT_LINE_COLOR, new RGB(225, 235, 224));
		
		store.setDefault(CompilationUnitEditor.PRINT_MARGIN, false);
		store.setDefault(CompilationUnitEditor.PRINT_MARGIN_COLUMN, 80);
		PreferenceConverter.setDefault(store, CompilationUnitEditor.PRINT_MARGIN_COLOR, new RGB(176, 180 , 185));
		PreferenceConverter.setDefault(store, AbstractTextEditor.PREFERENCE_COLOR_FIND_SCOPE, new RGB(185, 176 , 180));
		
		store.setDefault(CompilationUnitEditor.PROBLEM_INDICATION, true);
		PreferenceConverter.setDefault(store, CompilationUnitEditor.PROBLEM_INDICATION_COLOR, new RGB(255, 0 , 128));
		
		store.setDefault(CompilationUnitDocumentProvider.HANDLE_TEMPRARY_PROBELMS, true);
		
		store.setDefault(CompilationUnitEditor.OVERVIEW_RULER, true);
		
		WorkbenchChainedTextFontFieldEditor.startPropagate(store, JFaceResources.TEXT_FONT);