Just a note as this was almost IMPOSSIBLE to find information on. Hopefully it’ll help someone else.
Converting a small program from Arduino Uno to Arduino Yun, one of the functions is using a Serial connection. Works great on the Uno, will work with the Aruduino IDE Serial Monitor no problems. But won’t send data with X-CTU or Parallax Serial and my C# program can send data, but never receives data.
Fun. Well it turns out that Yun (and evidently Leonardo) requires you to use DtrEnable – otherwise you get undefined functionality.
Set DTREnable = true and everything works great!