Compile.log is generally more relevant....attacked small convoy of protected merchants from Holland: merchant pinnace, snow brig and raa frigate under spanish flag(playing assassin storyline). Forced the pinnace to surrender and suddenly my reputation got hit by 15 and two other vessels became neutral ...
Often your Ship's Log should contain an entry if large changes to reputation/relations occur, so you may want to have a look through that.
How did you force the Pinnace to surrender? Did you pound them with cannons?
If so, were you using Manual Aim?