I have a transparent BufferedImage created with the following code(not relevant how it is created, I think):
GraphicsEnvironment ge = GraphicsEnv
Got it :) used clearRect instead of fill with a transparent color.
graphics = (Graphics2D) offlineBuffer.getGraphics();
graphics.setBackground(new Color(255, 255, 255, 0));
Rectangle screen = transformationContext.getScreen();
graphics.clearRect(0,0, (int)screen.getWidth(), (int)screen.getHeight());