It looks as though Twitter has started to filter out Retweets (RT) from their search results. Now this algorithm change has only affected the "integrated search" algorithm according to @Charles (Twitter UX Supprt Team member).
What is "integrated search" exactly? It looks to reference the search box within your profile page. I tested the home page search box as well as search.twitter.com, but this functionality has not been implemented yet. @Charles goes on to further explain "RTs are usually a lot of noise in search results/ Excluding them makes the results cleaner and (in most cases) better.".
@RayBeckman posted, "Has @ Twitter Declared War on Traditional Retweets? #TR", about his disgust with the removal of RT from the search results. He points out that he is more upset that Twitter did it in a "..sneaky, slient, back-door way.". He has started a petition at http://twitition.com/2sri3 and urges Twitter users to use "TR" instead of "RT" to signify "Traditional Retweet". @RayBeckman also notes that "TR" has been used in the past to represent "Translated" tweets (which I did not know).
As of yet, the only official response has come from @Charles and the Twitter blog has made no reference to this change.