At WebmasterWorld, a forum member is baffled by the fact that his homepage isn't ranking for a relevant search term; instead, one of the internally-linked pages rank. According to the forum member, the homepage has the right keywords within the title tag and should be targeted appropriately, but the internal page outranks it.
It seems that this forum member is not alone. Another member encountered a similar issue recently. Other forum members suggest that it could possibly be a temporary thing, but if (after 3 weeks or so) nothing has changed, it may be helpful to optimize those pages again.
Another possibility could be over-optimization of the front page, which could result in a penalty as we've seen before. One forum member makes this case clear:
If it has taken a tumble on just a handfull of specific searches, and there is no legit reason for the inner pages to rank higher than the home page (ie they're less targeted and have a weaker link profile), then it sounds like your home page may be seen as a bit over optimized for the phrase(s).
Forum discussion continues at WebmasterWorld.

Comments:
gabs
08/13/2008 03:42 pm
its a penalty.. bad linkage/over seo'd/dup content..
Jaan kanellis
08/13/2008 07:30 pm
Actually I always ask the opposite question: Why do so many home pages rank for 2-3 keywords phrases when clearly it would be better from relevancy and end-searcher experience for the sub-page to rank?
Rob Abdul
08/14/2008 11:47 am
I have the opposite issue, my homepage ranks better for keywords that I’ve SEO’d for deeper pages. I know why. 1.My deeper pages change more often than the home page. 2.My deeper page are visited less than my homepage by googlebot.
No Name
08/14/2008 01:39 pm
thank you for sharing