Ubuntu – Mouse does not click in the focused window but the oldest window

I couldn't find an xorg setting, but I discovered there's actually a "rapid-fire" setting on the keyboard itself that was causing this. Turning that off fixed the problem.

I just had the same need and ended up here looking for a solution to the problem.

As it doesn't seem like something that anybody else solved anywhere else, I used my basic shell skills to create the following script, which does the job using xdotool:

# Get geometry information of the currently active window.
GEOMETRY=`xdotool getwindowgeometry $(xdotool getactivewindow)`                 
# Extract information about the dimensions of the window and divide
# both of them by 2.
DIMENSIONS=$(echo "$GEOMETRY" | grep -Po "[0-9]+x[0-9]+")                       
X=$(echo $DIMENSIONS | sed 's/x[0-9]\+//g')                                     
Y=$(echo $DIMENSIONS | sed 's/[0-9]\+x//g')                                     
X=$(expr $X / 2)                                                                
Y=$(expr $Y / 2)                                                                
# Move the mouse cursor to the middle of the active window.
xdotool mousemove -w $(xdotool getactivewindow) $X $Y

I've put this in a file and added a custom keyboard shortcut that runs it.