In debian/ubuntu, you'll need to edit the /etc/init.d/mongodb script. Really, this file should be pulling the settings from /etc/mongodb.conf but it doesn't seem to pull the default directory (probably a bug)
This is a bit of a hack, but adding these to the script made it start correctly:
add:
DBDIR=/database/mongodb
change:
DAEMON_OPTS=${DAEMON_OPTS:-"--unixSocketPrefix=$RUNDIR --config $CONF run"}
to:
DAEMON_OPTS=${DAEMON_OPTS:-"--unixSocketPrefix=$RUNDIR --dbpath $DBDIR --config $CONF run"}