I'm running Defragster's sketch from
msg #7.
To reproduce the problem, after uploading and opening the serial monitor (with Teensy Port selected), I quit and restart the IDE. When the IDE restarts, it automatically opens the serial monitor. If the sketch is already running with the LED blinking, nothing is supposed to appear. The sketch only prints stuff when the sketch starts running.
Then with the serial monitor open, I press the pushbutton on Teensy. Teensy Loader uploads the code again.
On the first pushbutton-triggered upload after starting the IDE, when Teensy starts running the sketch again, the serial monitor fails to connect to the freshly reprogrammed Teensy. Its LED stays on solid, indicating it's waiting for the serial monitor to open.
But if I first kill the serial-discovery.exe process, then press the pushbutton, after upload and Teensy begins running Defragster's sketch, the serial monitor does connect. The 2 lines appear (0.33 and 1.33 seconds on my test machine) and the LED blinks, indicating the sketch saw the serial monitor open.