I just ran into this exact same problem, with mouse sensitivity being insanely high in programs like ScummVM in fullscreen mode, but fine in windowed mode.
It appears to be a bug with SDL fullscreen when used with a touchpad.
Workaround - type this in your shell before running the program:
Mouse speed will be normal again. To make this change permanent, put it in your .bashrc file.
(BTW I'm using Slackware 14.0 on a MacBook Pro, with SDL-1.2.14).