If you made a tipped arrow with instant damage effect and shoot it, the damage dealt by arrow will be basic, instant damage effect doesn't deal additional damage.

The problem is the fact, that the arrow firstly deal its damage, starting an invulnerability of target, than apply its effect. Due to the invulnerability of target, instant damage effect doesn't deal damage.

There are two solutions for this: just like in combat test snapshots, make arrow don't start invulnerability timer; add effect's damage to the arrow, and make damage of the arrow ignore target's protection.