Admin’s Note: This solution was emailed to me by Bharath, as he was facing this problem and found a solution to this. If you want to drop a tip or a hack, just send me an email via the contact-me form and I might just publish it
Sometimes when playing native games in Linux they may appear transparent. This may feel good for some people. I felt games should be opaque so that the visibility of the game is more realistic and gameplay experience is better. I searched out Google, Compiz forums and even Ubuntu forums just to return without a proper solution. May be there is one out there in the internet and only its me who did not ponder over it. Switching off compiz-fusion may be one option. But switching off every time you run a game and switch it on after closing the game would be a frustrating job.