I think they are using registrar information.
I have a client that got hit really hard by Penguin.
They tried to repair their link profile without any effect.
We also carefully redid on page to focus on a single phrase.
In desperation we got a keyword rich domain name (the original was a branded one), but the client cross linked from the old site.
The new site will not even show for the domain keywords, something I have not seen before.
I am thinking that the penalties followed the domain name switch as registration details are the same for old and new.