I was having this issue for so long. I often download Linux ISOs to test and learn differences between them. I’ve got lots of old PCs/Laptops laying around and Linux is a great way to give them new life. When I reboot my server, Transmission wasn’t starting automatically, yet before the upgrade to 14.04, it was working fine. Fix below and reference.
transmission-deamon issue after reboot
The following removes the auto-start scripts that may have issues.
sudo update-rc.d transmission-daemon -f remove
Then the following adds them back. The 80 makes it start later in the boot process. The reason I needed this is to allow for networking and NFS to load completely before it starts.
sudo update-rc.d transmission-daemon defaults 80