I'm no longer a user of Ubuntu, but I suspect this issue is still relevant. The 
corresponding bug in KDE is here:
https://bugs.kde.org/show_bug.cgi?id=177495

A quote from there on how to work around this bug:
"You can disable unredirecting the following way:
1. open ~/.kde/share/config/kwinrc in an editor
2. go to section [Compositing]
3. Add following line:
UnredirectFullscreen=false
4. Save file and restart kwin (alt+f2 and kwin --replace)"

I suspect the issue is similar for GNOME.

>From what I can understand, the problem occurs because fullscreen
windows are unredirected by the window manager. This is done to improve
performance of fullscreen games and such. However, when a control
appears, the window is redirected again, which causes the flicker, and
then is unredirected again when the controls disappear.

I find the usefulness of this feature dubious. Most modern video drivers
use the DRI2 extension for X.org, which, as I understand it, should
resolve problems with redirected fullscreen applications. Plus, the
flickering is much more annoying than some performance drop.

** Bug watch added: KDE Bug Tracking System #177495
   http://bugs.kde.org/show_bug.cgi?id=177495

-- 
[i945gm] Video flickers in full screen while controls appear/disappear when 
desktop effects are enabled
https://bugs.launchpad.net/bugs/410837
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