I've got a site that has inbound links with anchor text "A" from sites pointing to the home page. The site is ranking for that term, but only the respective inner page is ranking for that...not the home page which is receiving the link.
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).
Look at relevant keyword density of these two pages and internal anchortext of the links pointing to the inner page. Also, if you have too many inbounds with similar or identical anchor text pointing to a specifc page you may have page ban for that search term. If that is the case dilute the anchor text.
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]
It took us months to get rid of a situation where an internal page was the only one returned by google - although the other SEs returned the home page as expected. It happened suddenly - about the time of a google update.
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 It was never designed as a content page, just a way for the visitor to access extra, out-of-date pages.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.