Emulator

Game Name?
Mario Kart Double Dash, but seems to apply to any game.
I have tried it on Super Mario Galaxy, Lost Winds and Zelda: Twilight Princess as well.

Game ID
Mario Kart Double Dash: GM4E01

MD5 Hash
Mario Kart Double Dash: 8f4b2434444a89ae345ecba99d2ac58d

What's the problem? Describe what went wrong.
When I try to switch back from fullscreen with Alt-return, it returns back into window mode and often (but not always) the game freezes. Dolphin as well as the whole desktop become unresponsive. I can still move the mouse cursor, but I cannot click anything anymore (see screenshots 1 and 2). One time with Super Mario Galaxy, the game music kept on playing, even though the game itself was frozen, but I have not been able to reproduce this effect.

Dolphin also freezes when I trigger certain Unity elements while on fullscreen. For example, when I change the volume so that the Ubuntu volume bar shows up (screenshots 3 and 4) or trigger the Unity Dash by pressing the windows key, while the game is running on fullscreen. If you think this is a completely separate issue, I could write another bug report for it.

In order to regain control of my desktop session, I have to switch to the linux console with ctrl-alt-f1, kill dolphin,
and restart lightdm.

What steps will reproduce the problem?
Start Mario Kart Double Dash (probably works with any game) and toggle between fullscreen and window mode a few times, until it freezes.

For the thing with the volume bar, just start a game, go into fullscreen and change the volume using whatever shortcuts your computer provides. This made dolphin freeze much more consistently than the fullscreen thing.

Which versions of Dolphin did you test on? Does using an older version of Dolphin solve your issue? If yes, which versions of Dolphin used to work?

Installed from ppa:dolphin-emu/ppa
dolphin-emu-master: version 4.0+git+r85~13~ubuntu15.10.1
dolphin-emu: version 4.0.2+dfsg-2build1

What are your PC specifications? (CPU, GPU, Operating System, more)

CPU: Intel Core i5-5200U
GPU: Intel HD Graphics 5500
Ubuntu 15.10

Is there any other relevant information? (e.g. logs, screenshots, configuration files)

Info that dolphin shows at the beginning of emulation:

Dolphin OGL Video Backend
Video Info: Intel Open Source Technology Center, Mesa DRI Intel(R) HD Graphics 5500 (Broadwell GT2), 3.3 (Core Profile) Mesa 11.0.2

I uploaded four pictures I made of the screen after it froze. All of them are from the game Mario Kart Double Dash. The first two are after returning from fullscreen. The third and fourth ones show the screen after changing the volume while on fullscreen.