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I've a somewhat similar problem. I believe that it is an issue with the tf, but this is the standard setup I got from the repos. I've a Turtlebot Clone. I am really wondering what could be causing this behavior, it is not like it is a custom build or anything. Below is link to the bag file of a run. I would really appreciate someones feedback on this.
http://dl.dropbox.com/u/36264864/second.bag