Why doesn’t the boot-time scan work, e.g. what happens when you schedule a boot-time scan, any errors, etc. what ?
What avast version do you have before 6.0.1289 and how did you update to this latest version ?

Has your system ever been able to do a boot-time scan ?
If it has worked before what has changed recently, just prior to it not working ?

It doesn’t boot from a hidden recovery partition, it runs from the normal drive, windows actually starts to load but the avast boot-time scan runs before completion of the windows start.