Changed initial alpha value of glClearColor from 1 to 0 which is set when Initialising the Display. This now matches expected OpenGL behaviour. Thanks to Ryanm for spotting this. If you use FBO's make sure your setting glClearColor properly.

src/java/org/lwjgl/opengl/Display.java

@@ -905,7 +905,7 @@ public final class Display {
 
 	private static void initContext() {
 		// set background clear color
-		glClearColor(r, g, b, 1.0f);
+		glClearColor(r, g, b, 0.0f);
 		// Clear window to avoid the desktop "showing through"
 		glClear(GL_COLOR_BUFFER_BIT);
 		update();