When I said that the "first method described in the tutorial linked in the wiki did not work", I was referring to the method which you have posted "https://github.com/sparkfun/Arduino_Boards/blob/master/README.md". This may have not worked as we were working on a school PC, which did not have Admin rights, and had to run over to IT support every time we needed admin permissions for installing drivers.
I am afraid that I do not currently have access to the boards, as Dr Herceg has them, and so I will be unable to try the method until I get back to school on Monday at the earliest. Unless Dr Herceg tries it himself.
As for machine specifics, I have emailed people to find out, but I know that we were running at least a very recent version of Arduino.
For the 1st qbcan, we never got round to uploading any code to it, as we were trying to get the Pro Micro Arduino package as this ("https://github.com/sparkfun/Arduino_Boards/blob/master/README.md") method didn't work. It was while it was attempting to get the correct arduino Pro Micro package, that Dr Herceg clicked Leonardo in the Arduino IDE, at which point it broke on attempting to upload the sketch. It was not compiling correctly, as we had numerous issues with getting the ProMicro package to work, (Invalid boards.txt, putting it in the wrong place, have the wrongly named folder structure, using the wrong version of it (we found 2)). It never got onto the uploading stage, as it never properly compiled, until Dr Herceg said it was a Leonardo, which made it break. I am not sure whether the code managed to upload as a Leonardo, as I was not right there at the time.
For the 2nd qbcan, Windows did not think it was a Leonardo, and the Arduino IDE was told that it was a Pro Micro as by that time the Pro Micro package had been correctly added to arduino IDE. I cannot fully remember if Arduino saw its COM as COMxx (Arduino Leonardo)), but I don't think it did. For the 2nd one, all the code was uploaded as ProMicro, not Leonardo, because I was scared that it would break if I clicked Leonardo, and it all was the 5v, 16MHz setting.
Thanks, and I will get back with the machine and software specifics as soon as possible, along with any progress on fixing it.