jkwong might be right (still unlikely), but it would help to know who you are using. I use a herja so my form doesn't him morale, so that won't ever happen to me.

Noob answer you don't want to hear (I would assume you checked over your formation several times):
Sometimes the runes rollback for me... i.e. I put them in place, but they don't update the effect. I have to refresh to see they are back in the rune inventory and place them again. Made my khan not have a righteousness and took me 7 rounds to notice...lol