I have the same problem as described at the top:
When trying to upload a sketch via the USB Programming Port the following error message appears:
No device found on /dev/tty.usbmodem1421
However, when I connect the Arduino via the Native USB Port the sketch is uploaded and runs just fine.
I am using an Arduino Due, Arduino IDE 1.5.4 and Mac OS 10.9 (Mavericks).
Would the problem in my case also be the Baud rate? If yes, how do I change it on a Mac?
I would be very happy about any help.