
By following the simple advice in andar's announcement sticky at the top of this forum, my problem vanished immediately and I'm now getting better than 300KB/sec on downloads with a sufficient number of seeders. I am posting this here instead of as a reply to andar's post to give it additional visibility until the resolution is more widely known or is covered in the program's documentation.
In a nutshell, versions prior to 1.x did not limit protocol traffic (overhead) when limiting data transfer bandwidth (upload bandwidth in particular). However, with newer versions when you severely restrict upload bandwidth you are also limiting protocol traffic which in turn can affect download speeds dramatically. By simply adjusting the upload bandwidth limits to 32KB/sec per torrent and 64KB/sec for all combined torrents, my download speeds have gone back to full throttle. These particular settings may not be exactly right for you - just don't limit your upload bandwidth so severely that it doesn't allow any reserve bandwidth for protocol traffic and you should be all set.
tgeer