Middle Cick is not reacting as supposed, I guess. I use TPT with the scale:2 modifier on a windows machine. It seems like the area where the middle click samples pixels from is not the location of the pointer. I can not check with a linux machine right now.
EDIT: If i see this correctly, the sample location of the middle click sampling is twice the x and y values of of the actual pointer location. Probably a scale:2 thing, right?