This question is almost the same as
with one difference. I'm using the GNOME Shell desktop in Ubuntu 14.04 and therefore, the solution given in the linked Q&A does not work.
Does someone know, how I can turn off the unresponsive warning and the graying out of the window?
The main problem is that Mathematica even in version 10.3 does something weird, when you have dynamic content and you move a slider for more than a few seconds. Somehow the desktop environment thinks that the window does not work anymore (although it does) and shows this warning in the middle of your work.
The most unfortunate thing is that when you press Esc, like I do in my IDE when I want a dialog to disappear, the whole program is killed and all unsaved work is lost.