Comment 1 for bug 1752707

Interesting! I run caffeine 2.9.4 (please install this from the PPA before going any further) on my Ubuntu GNOME 16.04 two-screen system without problems.

What happens when you use xdg-screensaver directly?

Try running, in a terminal:

window_id=`xwininfo | grep "Window id" | cut -d " " -f 4`

Now click on the terminal window, and then run:

xdg-screensaver suspend $window_id
xdg-screensaver resume $window_id

This performs the same steps at a lower level as turning Caffeine on then off again manually. If this gives the same problem as using Caffeine, then the bug is definitely not in Caffeine.