+1 to that. I do the same thing, as do most folk who want to maintain a clean hierarchy and clean folder names. uTorrent's behaviour prior to this was simple and it worked. With this new torrent naming logic, sometimes I get video files named with the torrent's name and no file extension, and, as mentioned by ezridroftp, I have lost the ability to specify my own parent folder name for multi-file torrents. Please consider bringing back the previous behaviour at least via an advanced settings flag.
I too had this same problem but only in one torrent. I have finished downloading it now (after restarting the torrent about 10 times). I think it might have something to do with a "Power Options" setting under control panel, specifically the "Turn off Hard disk after xx minutes". I have mine set to 20 minutes. But the other torrents work fine AND I didn't have this problem before 3.0... Another thing I hope gets resolved in this beta is the "Add new torrent" dialog forgetting its previous window size.