Quick update, three years later. I've spend several days trying to figure out why I couldn't enable any plugins, and turns out I had the same issue. Running FreeNAS 9.2.1.8, so I'm not sure if this has been fixed since then but I assume not though since it seems to be quite an obscure bug.
The long of it: I had originally set up the NAS in Hong Kong when I was there in October last year, and now I am in Melbourne, Australia. The NAS is for a small business, and it's been doing its job fine as a simple file server for its local network. I thought I'd try setting up Transmission, but for a reason unknown to me I simply couldn't enable the plugin after installing it. I tried enabling/disabling the jail, reinstalling the plugin, installing other plugins, fiddling from inside the jail, resetting the NAS, all for naught. Then after seeing this thread, I realised that it might have something to do with the fact that I had been using SSH tunnelling to access the Web GUI. I'm not comfortable leaving the Web GUI wide open to the internet, even with proper password protection, so I have been using SSH tunnelling whenever I wanted to make any changes. It looks like the whole plugins interface has trouble whenever you're not accessing the Web GUI directly. So I temporarily port forwarded the Web GUI port to the Internet, got Transmission up and running and closed the port off again.
tl;dr: plugins may not work when you aren't accessing the Web GUI directly.