I don't think this is a dupe of MC-87942 but I'm not sure. This more relates to MC-68247.
The Bug
When respawning the Ender Dragon, the beams will point up towards the center of the sky. If you don't have all the Ender Crystals in view, the beam will not show.
Ways to Reproduce
One way to reproduce this bug is to spawn the Ender Dragon using the Ender Crystal method and observe. Another way is to spawn an Ender Crystal and manually change the BeamTarget using /entitydata. You would have to use {BeamTarget:{X:,Y:,Z:}}. Make the beam about 20 or so blocks away. When the Ender Crystal is out of view, the beam will disappear.
affects 16w07a, please add "rendering" label