It's all changing, you are being penalised
'Times are a changing' and so are algorithms and search engines.
There is an confusing and contradictory element within the Google Webmaster guidelines that indicates that Google is going to penalise gateway and door linking sites, that deep link into another site and/or deeper into the current domain.
This bizarre ruling means essentially a menu button with textual link to a page within your existing site may be being penalised by Google as a doorway page.
What we would consider navigation, can now be interpreted as a 'doorway' link!
If you have seen a dramatic drop in traffic then this is one of the features by which Google is smacking you around the head with a wet haddock..........unless, of course, you advertise with them. Then seemingly front page links are all fine and dandy.
That is not to say the Google are giving extreme preference to advertising client over, but rather are penalising those sites without the resources of on site web developers and generous incomes who can maintain their sites to the strict orthodoxy of google's latest algorithms.
To say their latest models are giving preference to the large businesses is an understatement. Their policy, while laudable, is heavily weighted in favour of those capable of investing time, energy and money in their websites, while penalising the small businesses struggling to compete.
Watch this space it is going to get worse!