If you change your actions with the unit or turn previous to the one that is giving you trouble, it may have an effect.
One time I was pissed my knight died to an archer on a hill, so I re-loaded. When I came back the game asked me what to do with my galleon, which I had previously not given orders to that turn. I told it to go do something, went to my knight, and he beat the archer.
So I figure everytime you do something you get a different seed for your next act. I was curious and did that like 4 more times, my knight always died if I had him attack before I instructed the galleon, and always won when I had him attack afterward. Unfortunately I couldn't find a set of actions to keep both my knight and a caravel alive that turn. One or the other wouldn't win their battle.
And no, I don't know how to have the game randomize the seed other than this kind of thing. It seems it can't be adjusted as it could in civ3.