Utorrent is now full of malware/adware... and also runs like crap... so malwarebytes is probably correct.
I suspect you applied a new version of it when you rebuilt. People are constantly writing the Dime list saying it suddenly stopped working after an unintentional update.
Go back to about 2.2.1 and it should solve your issue.
http://www.oldversion.com/windows/utorrent-2-2-1-25302Don't let it upgrade (make sure you turn off that setting in preferences - and make sure that sticks since certain versions seem to ignore that setting).
OTOH as far as being security conscious if you put PeerBlock on your system then try a few torrent sites you'd be amazed at what you find (seems like at least half the peers are in China!
). So really the best approach is to strip an old machine clean, wall it off from the rest of your computers/network, and set it to do only torrents with nothing else on it.