fcron refuses to stop with start-stop-daemon –pidfile ${FCRON_PIDFILE} if there are multiple PIDs. Change the line in /etc/init.d/fcron to this instead:
start-stop-daemon --stop -n fcron
See man 5 fcrontab
fcron uses a dedicated user to run root commands (systab). vixie-cron uses root to run the commands as, and set it's own variables (see /etc/crontab) that override default environment variables (such as HOME). I like fcron better because it is more predictable and doesn't change things around. Debugging scripts that run as cron jobs is tricky, and the less surprises, the better.