I had seti@home running on my linux box with just under 3000 wu. I stopped it at the end of a wu and downloaded and installed boinc. I believe that I attached it correctly and started it up. On the screen over and over I got messages saying things that implied that there was no work to do. And that it was waiting to contact the server. Each time the wait got longer. after about 4 hours I shut it down and started the old seti@home back up which found plenty of work and is cranking along just fine. Any idea what I am doing wrong?
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Nothing, they simply underestimated the load that would happen when everyone switched over. They ran out of work units, but there seems to be plenty available now. It's suggested that you read the news on the front page of the site where all this was mentioned:

[url=http://setiboinc.ssl.berkeley.edu/sah/]http://setiboinc.ssl.berkeley.edu/sah/