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I have the exact same problem. A website in a very competitive niche, my site is #2 behind the niche leader on Google, on MSN my site is #2, again behind the niche leader. Yet, my site is nowhere to be found on Yahoo, I mean it's below 1000. I'm thinking it's a penalty for on page optimization factors. I don't care though, Google is where it's at. With the same position on MSN, I get about 20% of the traffic that Google sends me. I imagine Yahoo is the same, I'm not going to worry about it. Funny thing is, Yahoo crawls my site like crazy... hundreds of hits a day from their crawler, over the course of a month, it's tens of thousands. Forget Yahoo, keep working on and improving your site, and they may come around eventually, but don't worry about it.
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