I’ve had a fairly long-standing problem with applications painting onto the desktop when their window was not supposed to be visible, i.e. after I switched virtual desktops.
Here’s a Chrome bug describing this behaviour that someone else raised: https://code.google.com/p/chromium/issues/detail?id=350522
As mentioned in my comment there, this is not Chrome specific since I get the same behaviour with Steam. A recent screenshot: http://www.themel.com/overpaint.jpg - the window is an xterm, and there’s a white line where I’m typing the command to capture the screenshot, but everything else got painted over by Steam running on another desktop.
X.Org X Server 1.15.1, driver version 331.79, NVIDIA GPU GeForce GTX 560 Ti (GF114)
Any hints on how to debug this further would be greatly appreciated.