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I'm using transmission and if i forget quit it before i shutdown computer it checks torrents at start-up like when i kill it.

I don't know where is problem in Debian, GNOME or Transmission configuration. I use transmission as user, not via daemon.

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transmission-gtk or the daemon? –  grawity Oct 3 '11 at 17:25
    
transmission-gtk. It's written in question ;) –  Miro Oct 4 '11 at 17:57

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