If you have a Watch directory and you have all your .torrents there... probably the cause of pausing all your torrents is this line of code (on your .rtorrent.rc config file )

# watch a directory for new torrents, and stop those that have been deleted

schedule = watch_directory,5,5,load_start=/home/(your username)/(your download folder)/watch/*.torrent

schedule = untied_directory,5,5,stop_untied=

ps: If you delete a .torrent inside Watch directory then will pause the torrent in your client.