Programming Arduino in Eclipse

I have been trying to integrade the Arduino into my Java projects in Eclipse. I have used the following turtorial: An this is were I am experience problems. When I reach the final step and run the program. The Arduino reacts by blinking on the L and TX LED, but after that nothing happens. I works perfectly in the Arduino IDE. I am using Windows 7 32-bit, Arduino Duemilanove and Eclipse SDK 3.5.1.