After some research (and multiple run-ins with the same issue), it would seem that the problem lies with the rtorrent process crashing, which can be due to a number of reasons. The most common being: Removing large torrents, having a full disk, and a non-zero extreme swap (not sure what this means).
In my case, rtorrent crashes every time I remove a large torrent file, even if I'm not removing the data. This has happened at least 10 times now and my solution is to simply restart the service, or force kill it, or disable the service from quickbox dashboard, and then start it up again. If that fails I reboot the OS which seems to work.
I would like to know if there's a way to remove large torrents safely, If they're undergoing a hash check on slow servers it can take a long time to do (and it eats up system resources for other tasks).