A post on Polygon discusses a serious bug in Pillars of Eternity, though visiting the links they provide to the thread about the issue and Obsidian's reply bring up pages saying they are currently experiencing "scheduled downtime," so they may be busy fixing this at this very moment. In any event, here's an outline of the problem so you can avoid falling victim to it:

Pillars of Eternity, the crowdfunded throwback to the great Infinity Engine role-playing games of yesteryear, has a game-breaking bug that developer Obsidian is working to fix. Meantime: Do not double-click items to equip them to your character. Drag them to a slot in the inventory screen.

Double-clicking, for some reason, removes all passive, racial and permanent buffs — forever. While players may reload an old save and proceed just fine, obviously that forsakes any progress between that save and triggering the bug.

The bug is described at length in this thread on Obsidian's official forums. In this reply, an Obsidian developer says that they do have a fix for the bug and that they're "trying to make it retroactive, so it will fix any save games that have this problem."

If the bug strikes party members, removing them from the party and then adding them back seems to fix the problem. Others report that though passive buffs do not show up, they appear to still be present and working.