The one I'm battling at the moment is the configuration of my transmission jail.
I had set one up earlier but had to resort to command line to get it running. However, it would regularly shut down on its own (the jail) and transmission would report permission denied errors when trying to write files, but only sometimes.
Having learned a bit about how this is all supposed to work, I decided to delete the whole thing and set it up again from scratch, this time staying in the GUI.
I've installed the plugin and the jail is present, however the Plugins > Transmission menu is not present. I found this is due to a failure to communicate with the jail at the network level.
I reviewed the network config and found it set for DHCP (which worked fine on the original jail). I updated the jail's MAC address to match the original so it would use my DHCP reservation. Bouncing the jail a couple times had no effect -- ifconfig still shows the interface is without an IP address.
I rebooted the entire NAS box, but the jail still doesn't get an IP. I edit the jail again, this time putting in a static configuration, but the NIC remains unconfigured. When I go in to edit the jail again, the configuration is all gone and DHCP is enabled again.
I reboot the jail, then the entire NAS, manually configuring the jail again each time, but it still reverts to DHCP (which still doesn't work).
I open a shell in the jail and manually configure the interface and I've got communication (I can ping my desktop and the gateway), but it only lasts until the jail is restarted, and the Plugins > Transmission menu never shows up.