Thought append my solution here. Not really mine but took some time to find it and it worked for me.
Problem: Transmission cannot save files into data directory: Permission denied error. Run as nobody, permissions repaired, still no go.
This worked:
"Re: Permission denied
by endle
I was having a very similar issue, and also have scoured the web looking for possible solutions. Finally it dawned on me, so I wanted to post this here for posterities sake:
Currently, I have a seperate hard-drive mounted as /mnt/Downloads and then I sym-link to that from my home-folder.
After trying every possible configuration of permissions, I finally figured out that Transmission wanted the direct path to the Downloads folder (/mnt/Downloads) rather than my sym-link path of /home/me/Downloads
Once I did this, and then restarted transmission-daemon, the permission errors went away"
So in Transmission config I replaced //Downloads to //mnt/user/Downloads, restarted Transmission, success! :-)))