I can confirm the same happens with ut2004 and wesnoth (presumably this uses SDL?) − the mouse jumps to bottom-right corner in my case − and that exporting SDL_VIDEO_X11_DGAMOUSE as 0 fixes this.
However, to add to the wierdness, my own little test program is completely unaffected by this (setting SDL_VIDEO_X11_DGAMOUSE as 0 or 1 makes no difference either). This is just a small test program in various screen modes (with OPENGL & HW framebuffer enabled). Debian testing (nearly up-to-date); uname -r: 2.6.22-3-amd64. ii libsdl1.2-dev 1.2.11-9 ii libsdl1.2debian 1.2.11-9 ii libsdl1.2debian-alsa 1.2.11-9
