Oh, wow, really looks like something within the Arduino IDE. Wouldn't have guessed that!
Can you try one more test?
Teensyduino makes changes to Arduino's serial monitor. Maybe they're related? If you look at the title bar of the serial monitor window, it says "TeensyMonitor". That means you're running Teensy's modified serial monitor.
If you close the serial monitor window, then select a non-Teensy board in Tools > Boards, and open the serial monitor again, you should get the original serial monitor without Teensyduino's patches. You'll know it's Arduino's original version when the title bar shows only "/dev/cu.usbmodem2397461 (Teensy)" without the word "TeensyMonitor".
If that makes a difference, then I'll start trying to figure out what I might have done that's messing up the serial monitor. If both fail, then at least we'll know it's something deeper in the Arduino IDE or Java or JSSC. Either way, I really do want to get to the bottom of this, if you're willing to keep doing tests and help narrow down where the problem really is.
Of course I`m willing to keep testing and if I can I will help to isolate this Bug.
It does not change, in both cases TeensyMonitor: /dev/cu.usbmodem2397461........ is written in the title bar.
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