You are probably trying to set the discharge rate to something greater than the charger will allow. Just like you can't set the charge rate to a greater value than the charger will allow. On my little Turnigy 50 watt chargers, the MAX discharge rate is only 5 watts, so for a 4 cell battery, something like 300 ma. Not terribly useful. In order to get batteries down to 50%, it is much easier for me to give them a partial run and then put them on 'Storage' mode charge.
Which charger do you have? I THINK I can turn my 'time-out' feature off, but have never looked to be sure. It would still take too long to run them down to 50%, so I just don't use that feature.