A number of things can randomly cease to function. I've seen this with:

1. Passive class abilities (fighter's bonus PV, monk's bonus DV)
2. Active class abilities (says you don't have any extraordinary abilities)
3. Elemental shard powers (passing through walls, not drowning in water)
4. Passive skill bonuses (most noticiably the attribute bonuses from athletics)

In all cases saving and reloading fixes the problem, at least temporarily. Not all of these things necessarily stop working at the same time. So far I haven't been able to find what triggers this.