Looking into the internal links report i see that for our forum's main page it shows 1,086,567 links and for sites main/front page just 552,838. This can't be correct, all pages link to the front page but not ever page in the website links to the forum main page.
I am just afraid that this gives wrong emphasis to the site structure and is one of the reasons we saw a decline in google referrals to every section other than the forum.
Thanks for reading, any feedback and help will be highly appreciated. I tried to bring this up in google forums for webmaster tools but was not able to find any feedback there at all.