I've been having this problem too, since I set up my new blog a few weeks ago (my old one just defaulted to the post page as the front page). I just did a quick test, and discovered in my case, the stats for "home page" are actually the stats for the blog posts page. The stats for "home" are for the splash page.
My splash page is called "home" and my posts page is called "blog," so I'm still baffled as to where the "home page" comes from, but I just recorded my stats for the day on each page, then logged out and visited each page and refreshed them several times (counting how many times, of course) and went back and the new stats were just what I expected.
After I upgraded to 3.1, my "home page" link on the stats feed started linking to the splash page instead of wordpress.com, which is what was really confusing. Both the "home" and "homepage" links took me to the splash page, but now I know the stats numbers for "home page" refer to my page called "blog." (which has never shown up in the stats as "blog")