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Is there a reason for this? The site previously had a -950 penalty / backlink devaluation. This seems like an off-shoot of the Yo-Yo effect.
Usually I see it happen the other way around - inbound links to the inner pages causes the home page to rank for that term (in some cases).
However, there is an update going on so let things settle first.
[edited by: Pass_the_Dutchie at 12:49 pm (utc) on July 1, 2009]
We tracked it eventually to having two links for each menu item, one wrapped around a "bullet" icon which changed colour when the link was hovered over and the other around the actual menu link text. Removed the icon link and bingo!
Why did it happen? Another of google's fancies. The site had used the same technique for about eight years, suddenly they got upset about it and the site all but died.
The really odd thing was that the page they decided to display had about 30 words on it with fewer keywords than any other page and with a slightly different menu. It was never designed as a content page, just a way for the visitor to access extra, out-of-date pages. Why google dismissed the other links/pages and chose that one we'll never know.
To give google some (small amount!) of credit: they did list the odd page within the top 25 or so links.