it you are using the web interface I think I know what your problem is .
look in settings.json for:-
"rpc-whitelist": "192.168.0.35, 127.0.0.1",
<------- put in the ip address of the other machine there is also :-
"rpc-whitelist-enabled": true, -- False I think allow any IP to enter , but fully sure
I only connect to my Sheevaplug from one machine on a fixed ip of 192.168.0.35 , I think if you are not on the list you just get black listed
this is my transmission-daemon file :-
#! /bin/sh
### BEGIN INIT INFO
# Provides: transmission-daemon
# Required-Start: networking
# Required-Stop: networking
# Default-Start: 2 3 5
# Default-Stop: 0 1 6
# Short-Description: Start the transmission BitTorrent daemon client.
### END INIT INFO
# Original Author: Lennart A. JÃŒtte, based on Rob Howell's script
# Modified by Maarten Van Coile & others (on IRC)
# Do NOT "set -e"
#
# ----- CONFIGURATION -----
#
# For the default location Transmission uses, visit:
# http://trac.transmissionbt.com/wiki/ConfigFiles
# For a guide on how set the preferences, visit:
# http://trac.transmissionbt.com/wiki/EditConfigFiles
# For the available environement variables, visit:
# http://trac.transmissionbt.com/wiki/EnvironmentVariables
#
# The name of the user that should run Transmission.
# It's RECOMENDED to run Transmission in it's own user,
# by default, this is set to 'transmission'.
# For the sake of security you shouldn't set a password
# on this user
USERNAME=transmission
# ----- *ADVANCED* CONFIGURATION -----
# Only change these options if you know what you are doing!
#
# The folder where Transmission stores the config & web files.
# ONLY change this you have it at a non-default location
#TRANSMISSION_HOME="/var/config/transmission-daemon"
TRANSMISSION_HOME="/mnt/sda1/share/transmission"
#TRANSMISSION_WEB_HOME="/usr/share/transmission/web"
#
# The arguments passed on to transmission-daemon.
# ONLY change this you need to, otherwise use the
# settings file as per above.
#TRANSMISSION_ARGS=""
# ----- END OF CONFIGURATION -----
#
# PATH should only include /usr/* if it runs after the mountnfs.sh script.
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
DESC="bittorrent client"
NAME=transmission-daemon
DAEMON=$(which $NAME)
PIDFILE=/var/run/trans/$NAME.pid
SCRIPTNAME=/etc/init.d/$NAME
# Exit if the package is not installed
[ -x "$DAEMON" ] || exit 0
# Read configuration variable file if it is present
[ -r /etc/default/$NAME ] && . /etc/default/$NAME
# Load the VERBOSE setting and other rcS variables
[ -f /etc/default/rcS ] && . /etc/default/rcS
#
# Function that starts the daemon/service
#
do_start()
{
# Export the configuration/web directory, if set
if [ -n "$TRANSMISSION_HOME" ]; then
export TRANSMISSION_HOME
fi
if [ -n "$TRANSMISSION_WEB_HOME" ]; then
export TRANSMISSION_WEB_HOME
fi
# Return
# 0 if daemon has been started
# 1 if daemon was already running
# 2 if daemon could not be started
start-stop-daemon --chuid $USERNAME --start --pidfile $PIDFILE --make-pidfile \
--exec $DAEMON --background --test -- -f $TRANSMISSION_ARGS > /dev/null \
|| return 1
start-stop-daemon --chuid $USERNAME --start --pidfile $PIDFILE --make-pidfile \
--exec $DAEMON --background -- -f $TRANSMISSION_ARGS \
|| return 2
}
#
# Function that stops the daemon/service
#
do_stop()
{
# Return
# 0 if daemon has been stopped
# 1 if daemon was already stopped
# 2 if daemon could not be stopped
# other if a failure occurred
start-stop-daemon --stop --quiet --retry=TERM/10/KILL/5 --pidfile $PIDFILE --name $NAME
RETVAL="$?"
[ "$RETVAL" = 2 ] && return 2
# Wait for children to finish too if this is a daemon that forks
# and if the daemon is only ever run from this initscript.
# If the above conditions are not satisfied then add some other code
# that waits for the process to drop all resources that could be
# needed by services started subsequently. A last resort is to
# sleep for some time.
start-stop-daemon --stop --quiet --oknodo --retry=0/30/KILL/5 --exec $DAEMON
[ "$?" = 2 ] && return 2
# Many daemons don't delete their pidfiles when they exit.
rm -f $PIDFILE
return "$RETVAL"
}
case "$1" in
start)
echo "Starting $DESC" "$NAME..."
do_start
case "$?" in
0|1) echo " Starting $DESC $NAME succeeded" ;;
*) echo " Starting $DESC $NAME failed" ;;
esac
;;
stop)
echo "Stopping $DESC $NAME..."
do_stop
case "$?" in
0|1) echo " Stopping $DESC $NAME succeeded" ;;
*) echo " Stopping $DESC $NAME failed" ;;
esac
;;
restart|force-reload)
#
# If the "reload" option is implemented then remove the
# 'force-reload' alias
#
echo "Restarting $DESC $NAME..."
do_stop
case "$?" in
0|1)
do_start
case "$?" in
0|1) echo " Restarting $DESC $NAME succeeded" ;;
*) echo " Restarting $DESC $NAME failed: couldn't start $NAME" ;;
esac
;;
*)
echo " Restarting $DESC $NAME failed: couldn't stop $NAME" ;;
esac
;;
*)
echo "Usage: $SCRIPTNAME {start|stop|restart|force-reload}" >&2
exit 3
;;
esac
the bit you need to set is (TRANSMISSION_HOME="/mnt/sda1/share/transmission" )
which is the place it collects settings.json from :- eg
/mnt/sda1/share/transmission/settings.json
and this is my settings.json file in full.
{
"alt-speed-down": 150,
"alt-speed-enabled": true,
"alt-speed-time-begin": 540,
"alt-speed-time-day": 127,
"alt-speed-time-enabled": false,
"alt-speed-time-end": 1380,
"alt-speed-up": 5,
"bind-address-ipv4": "0.0.0.0",
"bind-address-ipv6": "::",
"blocklist-enabled": false,
"dht-enabled": true,
"download-dir": "\/mnt\/sda1\/share\/transmission\/Downloads",
"encryption": 1,
"incomplete-dir": "\/mnt\/sda1\/share\/transmission\/Incomplete",
"incomplete-dir-enabled": true,
"lazy-bitfield-enabled": true,
"message-level": 2,
"open-file-limit": 32,
"peer-limit-global": 160,
"peer-limit-per-torrent": 60,
"peer-port": 51413,
"peer-port-random-high": 65535,
"peer-port-random-low": 49152,
"peer-port-random-on-start": false,
"peer-socket-tos": 0,
"pex-enabled": true,
"port-forwarding-enabled": true,
"preallocation": 1,
"proxy": "",
"proxy-auth-enabled": false,
"proxy-auth-password": "",
"proxy-auth-username": "",
"proxy-enabled": false,
"proxy-port": 80,
"proxy-type": 0,
"ratio-limit": 0,
"ratio-limit-enabled": true,
"rename-partial-files": true,
"rpc-authentication-required": false,
"rpc-bind-address": "0.0.0.0",
"rpc-enabled": true,
"rpc-password": "{84f0367048091ed5bdb47e93f0aeaec30bbbc122deBhAWU\/",
"rpc-port": 9091,
"rpc-username": "",
"rpc-whitelist": "192.168.0.35, 127.0.0.1",
"rpc-whitelist-enabled": true,
"speed-limit-down": 400,
"speed-limit-down-enabled": false,
"speed-limit-up": 25,
"speed-limit-up-enabled": true,
"umask": 0,
"upload-slots-per-torrent": 14
}
My set up :-
/mnt/sda1/share/transmission/blocklists/
/mnt/sda1/share/transmission/Completed/
/mnt/sda1/share/transmission/Downloads/
/mnt/sda1/share/transmission/Incomplete/
/mnt/sda1/share/transmission/resume/
/mnt/sda1/share/transmission/torrents/
/mnt/sda1/share/transmission/watch/
/mnt/sda1/share/transmission/dht.dat
/mnt/sda1/share/transmission/settings.json
/mnt/sda1/share/transmission/stats.json
I use a number of cron job scripts , which I use to start downloading only at off peal times, read RSS feed and auto start them , move completeed file around etc.
ALSO MAKE SURE TO DO ANY CHANGES to settings.json WHILE TO DAEMON IS STILL RUNNING 
