I cannot tell, what is going on with Lion as I already upgraded to Mountain Lion, but the problem is still there.
'sudo killall -9 securityd' actually works for this perticular problem, but here's actually one quite unwanted side-effect - it is impossible to eject any removable devices after that from Finder - only way to do it is using hdiutil from command line using sudo. In addition to that using Directory Utility is also not possible in normal way - when Directory Editor is opened by admin user i.e. myself, then user is automatisally authenticated as root, but after this killing of securityd it is impossible to authenticate as root if root user is not enabled i.e. normal operation is not possible.
One more thing caught my eye as I use "Graphite" theme on my user interface (i.e. not the default "Blue" theme) - if these unlock authentication dialogs where appearing with "Graphite" theme before, then after killing securityd they were appearing in "Blue" theme - as if they were launched in context of different user than myself...
This all means, that we can cure the initial problem by killing securityd, but then we are causing new problem, which yet again is needing its' own cure - something else than restart. Maybe enabling the root user might help?
P.S. As someone stated before - I am also using Estonian ID card and the problem appears every time after using it...