I am having this issue since I swapped my main HD drive. I cloned my old HD to an SSD drive using SuperDuper. Since I've been using the new drive, the quarantine message appears for many applications every time I restart the computer, e.g. VLC media player, Xee, BitTorrent and others. I only have an admin account on the new drive, just as on the old one. I've browsed the net for solutions and I've seen that other people are having the same issue. I haven't found a solution that works for me though. I've tried reinstalling the programs and deleting their preferences files. No use. I have OS 10.8.5. Can anybody help?