Comment 49 for bug 1240957

A bit more testing (all on Ubuntu 14.04 as of 2014-04-01).

XFCE4 (apt-get install xubuntu-desktop): Windows get focused on scroll events, so this bug could not be tested there. Couldn't easily find a setting to turn that off (I assume it's buried somewhere though). Nautilus, gEdit, mousepad all scroll normally, but of course they all are focused and brought to the top of the window stack on the first scroll event. FWIW, mousepad installed on Ubuntu 13.10 under the regular Unity 7 desktop scrolls without focus just fine. I noticed it's a GTK2 app.

KDE: Kate scrolls without focus, but gEdit does not. (just had to check whether KDE native apps had a similar issue).

So it's basically GTK3 apps when not running under Gnome-Shell, and only with a mouse scrollwheel but not a touchpad, that have this issue with unfocused scrolling.