It appears I have a similar issue. I actually came from uTorrent and found the problem affects BitTorrent and qTorrent alike. It came out of the blue but might be related to my antivirus quarantining two files from my AppData/Local/Temp folder. I'm still exploring this. Meanwhile I found that, for uTorrent atleast, simply hitting the Enter button as if the popup window WERE there, it still loads the torrent. If I fail to do so immediately, I cannot do it afterwards and I get the 'torrent already in the list' situation. Eventually I find these torrents under 'hidden' (thank you Billyburu), and also, deselecting the Options pop-up under 'When Adding Torrents' bypasses the problem (unlike williamskevin), but the knowledge that apparently I had this 'invisible window' bothers me, especially since my virus scanner had picked up on something. Anyway, hope this helps, but also I'd like to find the source of this problem.