Sending them and their host a C&D letter from an attorney followed up by a phone call usually clears up most problems. Mentioning copyright infringement and loss of traffic/income of course. If that doesn't work -- Nice way: do as the post above mentioned, changing the content. But if they stole your content before, what's to stop them from doing the same again? Not so nice way: Go on a rampage and deindex their sites.
I'm a little confused here. Are you saying that they stole your content and because of the duplicate content penalty, they eventually trashed your articles search engine positioning? If that is the case, simply rewriting the content would solve the problem, right (even if it takes a whlie for the penalty to go away)? Not to undermind the ass pain that this is, but it's not like they stole your backlinks. Then again, for all I know, you have 1000 articles to rewrite. Brandon