The rootkit scan runs a few minutes after the desktop loads (it's a rootkit scan - looking for active rootkits (= hidden files, processes, ...); so, there's actually no point in trying to load as soon as possible, because if the rootkit is not yet active - it's not hidden, and it wouldn't get detected, at least not as a rootkit).
The boot-time scanner has also been improved, regarding the detection of hidden files (should the rootkit already be loaded at the time boot-time scanner runs).