Honestly, we're not going to do this - if apps advertise NET WMPING in their WM_PROTOCOLS they need to live up to the contract of responding to it in a timely fashion. The window is apparently responding to your mouse clicks, but it isn't responding to NET WMPING messages (the timeout is 5 seconds.) This is a Mathematica bug. One of the the red-hat dev-people wrote about it the following: This specific bug was already described here, here, here, and here. Especially, since it can only fixed for GNOME Shell by patching and recompiling Mutter. After accidentally killing my sessions several times and since I have to take care to move sliders only for one or two seconds, I'm super annoyed by this.
The most annoying thing is that when you press Esc to make the dialog disappear, then Mathematica is killed and all unsaved work is lost. In Mathematica version 10.3 and Ubuntu with GNOME Shell as desktop, you cannot move a slider for more than some seconds because than, a warning message appears saying that Mathematica is not responding and asking if you want to kill it. In Mathematica version 8, rotating a 3d graphics for longer than some second resulted in a graying out of the complete front end, indicating that Mathematica has become unresponsive. This misbehavior is present for a long time now and it is still not fixed in 10.3. Under Linux, the Mathematica front end does not handle window manager messages correctly. Finance, Statistics & Business Analysis.
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