Malware that seems to be able to evade avast!'s boot time scan includes pseudo rootkits (The type that employ a driver which is not itself hidden) and process injecting Trojans which inject dll's into Windows processes at startup. Both of these types of malware are detected by avast! in memory, but even a boot time scan won't remove them.
I've seen many examples of both on the forum.
There are more sophisticated malware removal tools available than a boot time scan: Ewido can detect and remove process injecting Trojans from memory- which is why it proves so effective against some stubborn infections on the forum- and Sysclean from Trend Micro will remove the registry entries that start up rootkit drivers and allow the malware to be removed, or at least it claims to be effective against the FU type rootkit infection. Certainly there are scripts available to defeat this type of rootkit by disabling the driver and removing registry entries- for example there is a script posted on the forum which will remove the rdriv.sys rootkit, something that a boot time scan certainly can't do.
Sadly, boot time scanning is no longer the last word in malware removal...