In my setup, pop-up windows and dialogs (from Atom) appear on the wrong monitor. I use 3 monitors left-middle-right, and the middle monitor is my “main” monitor. I run Atom on the middle monitor, but Atom’s pop-up windows and dialogs appear on the left monitor.
One such dialog is “Are you sure you want to delete this item?”.
My Atom is running in a Ubuntu environment. I direct the display output to my main machine, running Windows 7, via MobaXterm (a free X server for Windows).
According to ‘xdotool getmouselocation’ my Linux coordinates are 0-5205. My Atom main window is located around x=2000, which is on my middle monitor. Atom’s popup dialogs appear at coordinate x=0, y=0, which is in the upper left corner of my leftmost monitor.