Just a little background: My homepage was ranking in top 3 for most keywords. After penguin 3.0 my homepage disappeared from the search completely now. What happened now is that my inner pages are starting to rank instead at position 50-60 for the same keywords. My homepage has 95% of the links in my link profile. However the keywords that the homepage was ranking for were the inner pages keywords so the homepage was just an introduction with a button saying "read more". Could it be that its not a penguin slap but something else instead? Does penguin penalize the url only and not the domain?