Before penguin my site had about 1800 backlinks. A few days after penguin I noticed WMT shows me the site has about 240 backlinks.
The weirdest thing is, it's not that WMT suddenly doesn’t see more than 1500 links, it's that there are no external links to the home page seen there. None.
Most of the links we're to the homepage so it's a possibility that all the 1500 links that WMT suddenly doesn’t see, are all to the home page.
These links we're not deleted, that I know for sure (at list not all of them), and they can't all be seen as spammy. MajesticSEO can still see some of those homepage links that WMT doesn’t show me all of a sudden.
This could explain the reason why after penguin my site dropped for some of my main keywords which we're associated with my home page..
Any one encountered something similar?