I am having the same issue here.
I am on version 6.0.0.45, which is the latest as of Nov 3, 2016.
Server options state to set assets to non active if not seen for 30 days.
The only computers that have recently been set to inactive are ones that are subject to this option (which is enabled) - Set computers to non-active if disabled in Active Directory.
I still see dead machines showing up in reports where I have 'Where tblAssetCustom.State = 1'
Assets that should be inactive DO NOT have the 'Not affected by cleanup options' box checked.