http://www.devolution.com/~slouken/SDL/cvs.html
The X server was doing window shuffling when the keyboard focus was set on
the input window. This update fixes the occasional problems caused by this,
and only tries to go to fullscreen mode when the window gets keyboard focus.
There is an additional configure parameter: --enable-video-x11-grab
This tells SDL to enter fullscreen mode at the earliest possible moment,
and to grab the keyboard when entering fullscreen mode, effectively cutting
the window manager out of the picture. This is disabled by default.
I’m interested in feedback on the new code. Does it make sense?
Is it good UI? Try experimenting with it, and enable the keyboard
grabbing and see if you like that better.
Comments welcome. 
-Sam Lantinga (slouken at devolution.com)
Lead Programmer, Loki Entertainment Software–
“Any sufficiently advanced bug is indistinguishable from a feature”
– Rich Kulawiec