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.
WMT has been known to have bad data from time to time (that's putting it mildly) but this is a first for me and it makes me wonder if you do have a technical problem somewhere - such as a canonical issue or two giving some pages more than one URL. I'm admittedly grasping at straws here because I can't come up with a consistent scenario that would create the effect you describe.
If your traffic decline seems to coincide with the report of strange internal link numbers, I would start poking around in the reported URLs area. If there's a problem, it should show itself sooner than later.
Thanks tedster, g1smd. I did not have a canonical tag and the forum main page is indexed both as domain.com/forum/ and domain.com/forum/index.php. I applied the canonical tag and 301 redirect to the index.php version. I went through the website many times in hope of finding a technical error that would cause this miscalculation but so far found nothing.