I’m also working with Win and I switch the focus between schematic<–>pcb with the standard Alt+Tab hotkey. After that window-switch the “M” works correctly in the next kicad window (because that window got the official focus). Admittedly I have only a one-monitor setup, so the ALT+Tab switch is necessary.
Unrelated to the focus-thing: for the first footprint-distribution task try the new command “Pack&Move Footprint” (hotkey “P” I think).