I've had similar issues with my HD previously, a couple of times: whole 10s of Gb disappearing without a reason. It wasn't related to Torrent though, as I don't use this software. Anyway, it might help, maybe your problems are not related to Torrent at all on your machine either ?
For some odd reasons, I would end up with a HUGE log file in my library/logs folder (10-60Gb). No idea about the reason, some bad end of a corrupted file I suppose ? Anyway, the mess would clear up after some time, as the log wouldn't be archived anymore.
I tracked it down one day, by checking the size of my folders: which one was too big for its intended purpose. Maybe you can do that on your HD, to try to single out a huge temp file somewhere ? Its position might tell you which app it comes from.
Regarding the logs, check the archive logs. I think MainMenu proposes to clean up the archived logs anyway.
A.