Our script did cause some problems. We have a tracker on our board also, so there are times when a single IP will hit the tracker and if it's too busy at that moment, it sends the request again (and sometimes again and again, it depends on the bittorrent client) and so a few legitimate users did get caught in our IP tables. I did have a notice on the top of the board telling users that if they were blocked, to send me an email with their IP. I also flushed the iptables a couple of times a day.
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