Mmm -the error does not happen for me when I use box2d web...
If you move a physics object or set its angle directly using the same actions that you would use for a normal sprite, then the physics plugin interprets those changes as requiring a velocity inside the plugin (so, if you moved an object by 5 pixels to the right, the plugin would interpret that as a new velocity of 5 pixels / sec - even though it was 5 pixels in one tick, which would be 300 pixels / sec).
I was mistaken about the rotational velocity - I thought it also added a rotational velocity component but it does not... Moving objects that way should not really cause any problems in theory, but box2d doesn't always behave well when objects are continuously teleported to a new position or rotation, as would happen when you set the position / angle every tick.
In your case I would recommend making the pendulum static (immovable) and then you can place it / rotate it once and it won't move. Then, when you want it to fall, make it dynamic (not immovable) and then create the distance joint.