To confirm, I have (had?) the same issue, and the same fix works for me.

Update: This lessened the frequency of the crashes, but did not resolve them entirely - it's crashed around five times since I changed the setting. Any chance we can reopen this, or should I post a new bug report?

And as db48x mentioned, it wasn't an issue in .15.x.

That did it!

Thanks so much for the solution!

On 0.16.x in fullscreen, when focus shifts to another window (e.g. alt-tab, or a chrome notification), factorio will completely freeze. It crashes about 1/10 times focus shifts, and won't respond to anything but a "killall -9". Ubuntu 16.04, Factorio 0.16.07, no mods. I can upload the map,...

I'm using the latest 16.03 build on Ubuntu 16.04. When playing Factorio in fullscreen mode, switching between virtual desktops will occasionally cause Factorio to completely lock up. When this happens, it won't accept keyboard/mouse input and everything comes to a halt. After a few minutes, it goes ...