It seems that the Twitter API function that returns @mentions fails to return new-style retweets. I discovered this by accident after seeing references to tweets on my blog that TweetDeck didn’t show me in the @mentions column. I then looked on the Twitter site, and saw the same behavior there.
This seems like yet another problem with the RT API, and, like the lack of ability to add comments to a new style retweet, this behavior also seems unwarranted. It doesn’t really complicate the system to include new-style RTs of one’s tweets in @mentions, and it certainly makes for a more consistent interface.
If Twitter doesn’t fix it API, perhaps the good folks at TweetDeck could inject those missing tweets into the @mentions stream.