If the commands like Ctrl+Q, Ctrl+S or similar do not work in rtorrent, it is possible that flow control is enabled in your terminal/screen-session and you have to disable it!
Press Ctrl+A f in your screen session to disable.
Check the wikipedia article about flow control:
http://en.wikipedia.org/wiki/Software_flow_control
Discussion can be found at:
http://libtorrent.rakshasa.no/ticket/1611