Under Linux, the Mathematica front end does not handle window manager messages correctly. This misbehavior is present for a long time now and it is still not fixed in 10.3. 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 looked like that:

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. This looks like like that

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. 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. Especially, since it can only fixed for GNOME Shell by patching and recompiling Mutter.

This specific bug was already described here, here, here, and here. One of the the red-hat dev-people wrote about it the following:

The window is apparently responding to your mouse clicks, but it isn't responding to NETWMPING messages (the timeout is 5 seconds.) This is a Mathematica bug. Honestly, we're not going to do this [fix it in mutter] - if apps advertise NETWMPING in their WM_PROTOCOLS they need to live up to the contract of responding to it in a timely fashion.

If you want to reproduce the bug, just open a fresh Mathematica and type something like a=3. Now, just click on the = sign and hold the mouse button for more than 5 seconds.

Question: Is there a way to prevent this behavior in GNOME Shell? If not, is there a preferred Linux distribution that should be used for Mathematica?