HandleEvent() returns done each time it is called. If done was set to 0 the program should quit, but because done is not checked until *all* events are handled a following event can reset done to 1 and prevent the program from terminating when told to. I fixed the while loop that handles events to check for the state of done after handling each event. That could leave some events unhandled when the program exits, but it ensures that the program will exit.

#!/bin/sh
#
# Regenerate configuration files
cp acinclude.m4 aclocal.m4
found=false
for autoconf in autoconf autoconf259 autoconf-2.59
do if which $autoconf >/dev/null 2>&1; then $autoconf && found=true; break; fi
done
if test x$found = xfalse; then
    echo "Couldn't find autoconf, aborting"
    exit 1
fi