I’m not sure where the Jungo reference actually comes from - in the case with my Atmel ICE, it was one of the two Atmel drivers that was being installed that was the problem - as they were only meant to talk to Atmel Studio. I used zadig to replace it with the libusb driver, and I had not problems using avrdude to upload to MCUs on Windows since. And if I wanted to use Atmel Studio again, I would have just to reinstall the Atmel driver again, which was easy enough since it was included in the program install folder.
Try using avrdudess (as it’s a nice GUI for avrdude) and see if you programmer will talk to avrdude at all (you’ll be able to pick programmer options from the dropdown)… see if you can get it to detect the processor type on it’s own by hitting the ‘detect’ button (obviously with the target board plugged in!).