I've noticed this in previous builds, but I don't know why I didn't post it earlier.
When I run the Server Installer, it asks what user to run the server service as, but it does not actually set it with that user, it defaults to Local System. The Agent properly sets up with the supplied user.
This happens on both Windows Server 2003 R2 (enterprise x64) and Windows Server 2008 R2 Datacenter with SP1.