I have isolated this issue down to Eureka and Valkyrien Skies, although I have no idea why this is occurring.

If I kill the ender dragon, and summon another dragon, the crystals (that respawn) atop the obsidian towers will remain invulnerable and with their beams pointing into the sky. This makes additional dragons very difficult to kill as you can't get rid of the crystals (unless you are in creative mode).

Mods:
valkyrienskies-118-2.1.0-beta.12
kotlinforforge-3.12.0-all
eureka-1.1.0-beta.9

Can confirm, though I never would have guessed this mod would have been the cause. I also didn't realize they were invulnerable as I was playing in creative at the time.

valkyrienskies-1192-2.2.0-beta.2
kotlin-same
eureka-1192-1.2.0-beta.1