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The solution to this turns out to be fairly simple. It looks as if the velocity commands being output from move_base are either below static inertia or only barely above it (this is quite a big heavy robot). Increasing the velocities within TrajectoryPlannerROS seems to overcome the problem. It could be that the timeout is caused by a growing position error between the current pose and the reference pose along the planned path, which maybe has some bad effects upon trajectory planning.