It's unlikely that this is due to malware... but what have you been downloading via torrents? Torrents are most often used for downloading illegal content, such as stolen movies, music or applications. This is extremely risky behavior, for two reasons. First, this has been a means of transmission for Mac malware in the past, and is a constant source of malware for Windows. You simply cannot trust such things to be what they say they are.
Second, torrent clients may not respect the quarantine system in Mac OS X, and thus may provide malware with a back door to stroll through, bypassing all the built-in anti-malware security Mac OS X provides. (I do not know personally whether Transmission is one of those.) So if there is some bit of malware rattling around on torrents, you could easily end up infected.
Regarding the repeat disappearance of the app, that's not likely to be an effect of any kind of malware, even if you were infected with something. Are you absolutely sure it's actually gone? Try searching for it. Does anyone else have access to your computer? If you are downloading illegal material, is it possible someone you know is repeatedly deleting the tool you are using to do so in hopes that you will stop?
