I agree entirely! that's what makes me suspect that the infection is externally sourced from media or a portable device. Even so, it still shouldn't work these days.If 2 year old threats are still giving you trouble, something needs to change.
Unfortunately I don't have a copy of any of the conficker variants to experiment with, but I would expect Avira and the interactive module of AdAware to spot and block them.
What I don't quite understand is why the Windows auto-update hasn't resolved the issue?