I had the same issue happen and i found the solution. Lower your max connections to 1024 and see if all your torrents are ready ( not paused ) if they are ok, then it is an issue with the max open connection settings being too high even those they were modified in the config.. If you want to test if thats really the issue before changing it to 1024 kill the torrent process and run rtorrent out of screen by just typing rtorrent ( if max connections is the issus you will see a couple messages on the window saying "too many open files blah blah" ) then for sure thats the issue, set it at 1024 and start to go up gradually until you hit that error again, then you will know which is the max u can use.