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Steve,

This has occured to me when there are two non-adjacent links that are close to each other. They may be collision free in reality, but the coarse collision models often aren't. On industrial arms, this happens in the wrist quite often. If this is the case, you should be able to disable collision checking (assuming that this is safe).

FYI...I've created a walk through for industrial arms ( http://ros.org/wiki/Industrial/Tutorials/Create_a_Arm_Nav_Pkg_for_an_Industrial_Robot ). This may have information not in the standard tutorial.