I got exactly the same problem! I was using the Arduino Uno board with an Jtag ICE mkii for debugging which was working nice. As I begann to use the UART it was a heavy mess. The transmitting from Arduino to an external TTL-USB adapter was working but not in the other direction. I played hours before I saw this thread and that gave me the idea for looking into the shematic -> Bang! I saw the two resistors. Lesson learned: Do not use the Arduino hardware without the rest of the tools! Thought it was a good idea to use the hardware for rapid development. Now it costs me more time that I thought...
By the way the Arduino Nano is just different in this matter!