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Well, this is more sharing experience that a real answer, but it's too long for a comment; sorry a lot.
I have been playing around with the bag files recorded together with the video, and jumps follow this pattern: the robot rotates, pointing the kinect to unknown area, some scan matching fails (Scan Matching Failed, using odometry. Likelihood=-4266.67), so gmapping relays on odom, and when the rotation finish, filter updates but position is wrong. This is due to the narrow fov of kinect; same test with a laser works fine. So a possible solution is to be careful when building the map so the kinect pov don't move fast to an unmapped area. Doing full spins also helps a lot, as it compensates the narrow fov. And also tweaking some parameters helps (reduce angularUpdate, increase particles...), at the price of more CPU usage.
That said, the problem shiloh has looks like something different, related to tf failure. So shiloh, can you verify that odom -> base transform is correct?
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