hmm .. I got rid of little snitch, found it annoying as hell. lol
For each connection LW makes or attempts it will wake up little snitch. That includes files attempting to connect to hosts, let alone LW attempting to connect to ultrapeers when it starts up. Also, if you are downloading any torrent files, then you may get an endless supply of queries from little snitch. I suspect you might have some unfinished torrents.

I had similar issue with any p2p appication when using little snitch. And I hate being 'nagged' on my own computer.