I've been running my site with a child theme of Thematic Feature Site, but with the home page set to show posts rather than front-page.php while I figure out how I want to use it. When I upgraded to WP 3.0 beta 2, the blog started showing that file in all it's unedited glory.
I suspect this is because the "look for front-page.php " function has been integrated into the core as a default, and is overriding the settings under "reading." Solution: I changed the file name to featuresite-front-page.php and everything is as it was, waiting for me to hack it into whatever shape I want it to take next... ;-)