Thanks to this thread for helping narrow down the cause.
Essentially, every few seconds (I would assume three), Chaos bolts will drain mana and play an animation but release no projectiles, and thus deal no damage. Since you’re often weaving other skills in between, this results in the skill misfiring 1/2-2/3 of the time, at a rough estimate.
Removing the specialisation node “The Burn”, which extends Cthonic Fissure & Infernal shade durations when Chaos Bolts is cast, on a three second cooldown, appears to resolve the issue completely. So I would suspect some aspect of this node’s activation is preventing the ordinary function of chaos bolts, or perhaps not working entirely - I haven’t been able to determine if it does still actually extend the durations.