tedster - 5:20 pm on Jan 25, 2012 (gmt 0)
Over several years, it seems like there has been quite a struggle to generate an algorithmic result that does a good job choosing between a home page and a key internal page. I've struggled with both situations - the home page ranks when it's not the best landing page for the query, or the home page isn't returned when it WOULD be be best landing page.
This gets complicated by the fact that sometimes a home page seems to disappear for no clear reason or obvious penalty situation. We see this even in the site: operator results, and I sometimes suspect a bug in Google when domain roots get imported into the "full" index from a dedicated "domain root only" list.
Several years ago we had a discussion here that watched that kind of thing happen during various updates. In recent times, I've seen less of it but I think it's still a problem, even if there is no true penalty going on for the home page. And then - there can be a true, keyword-specific penalty against just home page. That would be what people call an "over-optimization" penalty, or the kind of thing that used to create a "minus 950" ranking.