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So, from the PDF you posted, it looks like whatever you're using to publish the "map" frame has indeed stopped publishing as no "map" frame exists in your TF tree. What are you using for localization? Also, "kinect_depth_frame" doesn't seem to exist in your TF tree. Perhaps you should be using "kinect_depth_camera" or "kinect_fake_laser" instead? Are your LaserScan messages stamped correctly? What node are the message filter warnings coming from?

Also, it makes sense that the costmap timeout would occur before the connectivity error, because the connectivity error is essentially the same thing just with a longer time threshold equal to the TF cache time.