Switching between windowed mode and fullscreen seems to be broken in 0.1.8 under Linux, or Ubuntu at least. I have tried on both Ubuntu 14.04 and 16.04 (two different computers, but both are laptops with Intel integrated graphics).
Here's what happens: pressing Alt + Enter doesn't switch between fullscreen and windowed mode reliably. Instead, it makes the screen do a weird flashy thing almost as if it switched to fullscreen for an instant and then switched back to windowed mode. If I try pushing it over and over again, eventually sometimes it will go into fullscreen mode. From there I have just as much trouble getting it back into windowed mode.
it seems to happen the same regardless of which fullscreen_method I use in config.txt
EDIT: issue still present in 0.1.9 fyi
it's working fine with Linux Mint (which is ubuntu based). Yet, on a laptop with Unity and ubuntu 14.04 (and I thing intel graphics), I have the same as you, it's flashing and can't stay full screen (so I just use the maximize button, it's not full screen but better than nothing).
I'm having another problem with linux mint 17 cinnamon:
with fullscreen_method 0 ('safe' default on linux), the screen is off-centered to the right & bottom, desktop still appearing on top & left. methods 1 and 2 work as they should. same thing on two different laptops with different gpus (intel hd & older nvidia).
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