Well the structure is different I would give it some time till google can make the adjustments, from what I heard it can take a while, even months. And if you have 4.0 cms also pay attention to the cms setup compare to the forum setup with meta tags, if your not using the cms just disable it . try VB ceo, I heard it is a great software and I believe it is free for 4.0 so this should give you a boost. There is a paid version but I have not found out what more dose it give you.
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