Occasionally the root homepage gets replaced with a random RSS feed from a specific blog. I have no idea how this happens and it hasn't happened to me but has happened to multiple people, so it is difficult to diagnose what is going on.
What exactly is the "Extra Homepage Checks" option for and how does it interact with a multisite environment? It is currently not turned on because I don't turn on strange features until I know what they are supposed to do.
This is on WordPress 3.0.4 multisite with WP Super Cache 0.9.9.8 (latest).