Does it also lower reputation if I raise Kalah as undead? IIRC, one has to kill him immediately afterwards, so people wouldn't neccecarily know you did what you did, would they?
Helping Logan instead of the rival families in Trademeet will raise virtue but not reputation. Various cases of freeing slaves, notably those in the Drow city, also do this, as does freeing the Djinni in the underdark. In UB, wishing to raise Kalah will increase virtue but actually decrease reputation.
Those are the only examples I can spot at-a-glance.