Synergy: http://synergy.sourceforge.net/
I'm running Gentoo Linux, with fluxbox as my window manager.
Anytime dosbox tries to go fullscreen be it invoked by alt-enter or set in dosbox.conf, and synergy is running on the same X server, dosbox begins the fullscreen process, grabbing the screen and changing resolutions, but then hangs at a black screen. Starting a new X server and running dosbox in that, or killing synergy, works around the problem.
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dosbox doesn't communicate with the X server itself.
It goes through libSDL.
Do other libSDL application work when you run them fullscreen ?
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UT2k4 works, though I'm not sure if it uses SDL only for input or if it opens its OpenGL context using SDL. Do you know of any SDL applications that for sure use SDL for video?
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http://lgames.sourceforge.net/index.php?project=LBreakout2
This one does. But not sure if it uses sdl in the same as dosbox does.
dosbox doesn't use the opengl context unless you specify it in the configuration file of dosbox.
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lbreakout2 exhibits the same problem. This must be a bug in SDL.