Had this happen most recently with a multiclass fighter 1*/warrior monk x: at a certain point (maybe around level 9, not 100% sure) the character stopped gaining the benefits of the +40% PV fighter ability. Maybe it's related to multiclassing, but I'm pretty sure I've seen the same thing happen with the ability to negate the DV penalty of body armor on a pure fighter. In both cases the ability is functional when learned and disappears at some later point.

EDIT: It seems that saving and reloading causes the class features to resume working correctly.
EDIT2: Had the same thing happen with the monk DV bonuses; stopped gaining them at some point and reloading fixed the issue.