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(I have not used chains yet as I do not fully understand them) [..] make Rviz crash with this error in the terminal window.
I don't know why exactly, but RViz and / or MoveIt has a tendency to crash when manipulators are defined as collections of links / joints. Using a chain seems to work around that.
There is an interactive marker associated with the 'arm' planning group in Rviz, but when clicked and moved, the gripper will float away with the marker and the arm stays in the same pose.
In your original description, you state that the iArm is a 6dof manipulator: the URDF you uploaded seems to specify only 5 joints. KDL doesn't work very well with anything < 6dof and you use the KDL kinematics plugin for your arm group (kinematics.yaml in your MoveIt package). I expect things to start working once you add the 6th dof (and regenerate your MoveIt package). Alternatively, you can ask MoveIt to do IK for your current URDF, by checking the Allow Approximate IK Solutions checkbox at the bottom left on the Context tab of the Motion Planning display in RViz.
In any case I'd also recommend generating an IKFast plugin for your manipulator. Such a plugin would also allow 5dof IK to work with MoveIt.
If the gripper planning group is chosen then the marker disappears. I am using the chain method in the Setup Assistant (base_link >> link5 for 'arm' group & link5 >> gripper for 'gripper' group).
One thing to check is that you don't have any overlap between the two groups (see Ioan Sucan's answer in End effector not found on the moveit mailing list). From your description it would seem the two groups share the link5 link.
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