I have had similar experience with Transmission, plus I think that Transmission doesn't offer a whole lot of options to configure the client...
So I replaced it with utorrent for Linux (http://www.howopensource.com/2011/08/install-utorrent-in-ubuntu-fedora/). I'm a happy camper ever since. You could give it a try if you're not desperately fixed on using Transmission as your torrent client.
If you're familiar with the Windows version of uTorrent, you won't quite get the same, be warned! Instead, a utorrent daemon is loaded that you can access via your browser. You have a lot of the same options in Linux, but not quite the same amount. The nice thing about it though, is that it's completely ad free (or is it my ad block that kills the ads?).
In any case, the utorrent daemon seems to run a lot smoother than the transmission client that comes as a default with Ubuntu.