Just came across this, and mildly excited someone else is using transmission with flexget!! Nice guide too.
I have issues with transmission, and flexget integration

I had flexget working with deluged (daemon) on my headless 10.04 64bit server, and it (flexget) passed torrents directly to deluge, which would download them, and nicely sort them into folders (say TV/show/season/episode.avi). Wonderful.
BUT, deluged was painfully slow downloading (maybe 200KB if I was lucky, usually much less), even after following wiki and posts to optimise it, so I wanted to try transmission. I then installed transmission-daemon and it chugs down at my capped 1500KB rate smoothly by default! So really want to stick to it, but I have issues:
- cannot use the transmissionrpc plugin for flexget. I easy_install it, seems fine, but always get 'unknown plugin' for it. Tried 5 different ways to config it from wiki, cookbook and other user posts, which all supposedly work. Wrong path?
- transmission won't move completed downloads to the download folder. I set it up to use temp folder, it does, then leave 100% files there, even after seeding to ratio. Enabled in config. Have seen a commend to remove them, but need to know how to work it in nicely.
- some downloaded files complete and then just pause (???)
- transmission won't remove torrent files from watch directory if just put in there by nautilus, or flexget etc. Will remove if added from the GUI though (I have a basic gnome desktop on my server to VNC in to). Config error?
- not sure if removewhendone is an option for 1.93. The below tvnamer script can move files out, but they're left in the GUI to be manually deleted. That's crap.

Anyway, and advice on any issue would be much appreciated!!

Also, recommend looking at tvnamer as an addon to rename files. Works a treat! And cam copy to another drive also, and file in appropriate structure. Not perfect script yet, but damn nice start. I used webmin to set up cron jobs for flexget & tvnamer regularly.

Please help me get flexget & transmission working properly!!
Ta.