I thought my previous post had answered that - maybe I've misunderstood the intent. All three devices were on the same hub, so removing it would have removed the problem because none of them would be connected.
I've moved the Duemilanove to a separate USB port and if I unplug or plug in the remaining two ports that are still on the hub (Nano and USB-TTL serial) they do not disturb the Duemilanove and unplugging the Duemilanove doesn't disturb the Nano.
Starting up the IDE still reboots both of them.
I found a thread about Serial port enumeration and I tried switching that off in each port and rebooting. Unplugging one Arduino doesn't reboot the other but starting up the IDE still reboots them both. http://arduino.cc/forum/index.php/topic,39770.0.html
Pete