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.