Bukkit

An item added with health_boost when player opens then closes inventory the buff is reset and it takes all the added hearts that the player healed away.

Using version 1.4.0

Just an idea to maybe fix it, Use an array of what the player has and compare it to one after the player closes inventory and only remove effects that need to be rather then removing all of them and reapplying them.

try to disable 

addEffects.inventory

from config.yml