Comment 85 for bug 153204

I'm upstream too. :)

When you first start compiz it has to redirect all of your windows so it can manipulate them. Unredirect Fullscreen Windows makes compiz stop managing the fullscreen window. This also puts the fullscreen window above everything else so all the windows compiz is managing will always draw underneath it. When another window pops up the only way we can show it is to redirect the fullscreen window again. This is the cause of the flicker, the window disappears while compiz is taking over drawing of it.

This option is only useful for drivers that have a naive implementation of GLX_EXT_texture_from_pixmap, modern drivers implement so called "zero copy" texture from pixmap so redirecting the window for compiz to manage it is basically free.

So while flickering is not the intention there is also no way to stop the flickering while this option is enabled.