This seems to be related to #153204.
Could you check if the following workaround works for you?
Type the following line in a Terminal
sudo apt-get install compizconfig-settings-manager
Start Advance Desktop Effects Settings (System->Preferences->Advance Desktop
Effects Settings).
Click on "General Options" under "General", uncheck "Unredirect Fullscreen
Windows" (should be 3rd from the bottom).
Click on Back and Close.
Does the flicking still happens?
** Changed in: compiz (Ubuntu)
Status: New => Incomplete
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Fullscreen games flicker in Ubuntu (GNOME only)
https://bugs.launchpad.net/bugs/224893
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