This is how I keep my bittorrent / utorrent running smooth and more secure than a default install. Make sure the port you are using is between 10000 through 65535. ISPs tend to throttle the lower ports for torrents.

I recommend using uTorrent 1.6.1 Build 490, apparently this was the last version created the orginal creator. You can download it here

In your settings there are a few things to adjust. First we are going to open up the preferences menu.

Click Options
Click Preferences

Now we are going to disable some peer sharing options

Click Bittorrent
Adjust the settings highlighted like the above image.

Now lets enabled ip filter to block known bad users.

Set ipFilter enable to true

I found a script that will auto update the ipfilter.dat file. You can download it here. This is a self extracting WinRAR script that will add the ipfilter.dat file to %AppData%\uTorrent\ and place a shortcut on your desktop to update the IP Filter block list. If you run the script when utorrent is still running you will need to disable and re-enable ipfilter in uTorrent for it get the new data.

I personally delete the shortcut on my desktop and create a schedule task to run the .bat file daily.