Maybe not directly relevant, but an observation on internal links:
I have a logo in the top left corner of every page which is a clickable link to the home page. Formerly I used my main keyphrase as the alt text. To reduce keyword densities I deleted the alt and left it blank.
After this I noticed in WMT that the internal links recognised for the home page started to drop off significantly - even though there's a text link to the homepage at the top of my side navigation (which is below the logo).
I filled the empty alt on the logos with the site's "brand-name" (primarily to increase brand name against keyword density). Now the internal link count for the homepage is increasing again.
On the face of it this looks like internal links have to pass some kind of quality test or they get discounted...? Which would isolate the target page and reduce its perceived importance within the site with a knock-on effect on ranking?