Posting to confirm the bug on my end as well. Happening on Fedora 17 x86_64 (Gnome 3 desktop) on a 560 Ti.
I can reproduce this with all of my SDL games, but I can't seem to get a screenshot of it... basically, any SDL application that gets focus will cause the entire desktop to tint dark blue, except for the mouse cursor. Putting focus on another window will remove the tinting until focus is back on the SDL application.
This seems to happen regardless of whether or not it uses OpenGL (tested with Eversion's software renderer and libSGE's software-rendered examples). You can get the libSGE examples here, if you want to try it out for yourself: