I also hear this, and it seems to have gotten louder with the 5.0 firmware?? When I switch presets, sometimes I hear several small glitch/click sounds. If I have a delay and other effects on the MF, the effect is of course
magnified by the effect. I've already tried different USB ports, cables, hubs, and have a robust power filtering solution for ground loops, etc. (I use a Furman IT-reference 15i to provide power for all gear)
This isnt a HUGE deal depending on how I produce, but if I ever want to change presets during a live set, this would be a problem.