These are my specs;
Slackware 14.1 x86_64
Nvidia GTX660M - drivers 331.67
I noticed in i3 when closing Geany the window has a tear or flicking effect.
I also use compton, but I noticed even without compton running Geany still tears and flickers slightly when closing.
I have a lot of various GUI apps I use GTK2/GTK3 & QT and I've never seen any GUI act in this way until I started using Geany a few months ago.
I created two small videos showing Geany tearing and flickering slightly when closing, and every time Geany does this, it's always with black appearing in it, regardless of my wallpaper background which isn't black.
This video is very short and it happens very fast, but if you watch it a few times you'll notice as Geany closes it turns black and also shows like a white line about in the middle going from top to bottom;
In this video I placed Geany on top of the SpaceFM file manager, I noticed when you close Geany on top of a window it flickers and tears in different ways.
I personally don't think this is some sort of driver or X rendering issue, if that was the case I'd see this more often in other applications and I don't, as I mentioned I've never seen this before, only in Geany.