To add a +1 here: I just finished the build of my QMX Rev. 2 and it has the same side tone clicking issue described here. Several factory resets and firmware re-installations (I installed 11, 12 and 14) didn't help. I also tried to play with the settings, however I whenever I find a setting with which I can send CW without being distracted by the clicks, I don't hear the opposite station anymore because I had to turn down volume too much.
I also tried the exact stepts Rasmus SA5RJS described. It sadly didn't change anything either.
One think I noticed that has not been mentioned here: When the device turns on after a factory reset, right before the menu to set the built version (80-20 or 20-10) appears, I hear the exact same click - without touching the paddle at all.
Thanks for all the work and 73 de Beni HB9HNT