I have suspected this for a long time.
Problem is, good document structure seems to be interpreted as "over" optimization.
file-name == <title> == <h1> seems to be a no-no. Add in proper use of <hX> tags and relevant internal anchor text and its all over.
There is nothing abnormal about a site designer having www.example.com/widget-books.htm point to a page named <title>Widget Books</title> that begins:
<p>A close examination of the literature about widgets reveals...</p>
<h2>The Widget Tablets of Samaria</h2>
<p>Preoccupation with widgets stretches into the distant past, with the first written reference appearing on clay tablets excavated from...</p>
which is found by way of a menu item that looks like:
<a href="http://www.example.com/widget-books.htm">Widget Books</a>
But, it appears that the learned engineers at Y have determined the above to be a sign of over-optimization and therefore penalize the page/site.
However, a site named widgets.com with a page named books.htm might well rank very nicely - even if there are no books, or references to books about widgets!