I'm still suffering from the problems I described in this post, and since I can't find a solution I've come up with a workaround. I'm thinking if I can use cron to schedule a restart of the transmission-daemon service on reboot then it will automatically load up the correct settings.json file and solve the issue. I can write the cron script, but I don't even know how I would go about writing the script that cron would call to get transmission-daemon to restart. If anyone has done anything similar or could point me in the direction of a tutorial that explains it I would appreciate it.
sudo grep transmission /var/log/*to see if it has indicated any problems there.