Bingo! I've managed to get this working in a brand new jail using the 6 following steps (for anyone who might be interested or having a similar issue):
1. Create FreeNAS jail (default settings - I called it calibre-server)
2. Enter shell of new jail
3. Run 'pkg upgrade' and then 'pkg install calibre'
4. Add storage to jail (i.e. mount the location of your Calibre library to the jail - I just used /mnt)
5. In the WUI create a Cron Job with the appropriate flags (mine looks like jexec calibre-server calibre-server --with-library="/mnt" --port="8282" --username="username" --password="password")
nb: the first calibre-server is the name of your jail!
6. Run the Cron Job
Browse to the IP (with appropriate ":" port number) and after entering your username and password your books will appear!
