I am also having a problem with the serial monitoring capabilities of the USB programmer on Windows 10.
I am programming an Arduino Duemilanove. It has nothing connected to it other than the programmer and a USB cable for power and I am testing using the example blink sketch with just a Serial.begin(9600) and single Serial.println in the loop.
What I’ve observed:
I can upload programs fine over ICSP from the Pololu programmer, but then am unable to successfully read from the serial port. In the Arduino IDE I am setting the board to be a Pololu Orangutan with 328p. Gibberish comes out, or nothing. Same outcome happens if I set the board to Duemilanove and manually upload the .hex file to the Arduino using avrdude over the ICSP COM port: light blinks per expectations, serial port reads nothing or gibberish.
When I restore the Arduino bootloader and upload over regular Arduino USB using the Arduino IDE and the board set to a Duemilanove, the program also works and I can monitor the serial port output either using the Arduino USB COM port or the Pololu serial port (TX to RX, RX to TX, Ground to ground) just fine.
I’ve tried removing anything having to do with COM or Serial ports (had a number of drivers from Adafruit and FTDI) and reinstalling the Pololu tools/drivers. Same results.
Loopback testing (ground to reset, tx to rx, echo user input in terminal) works fine.