What do you have the villager doing? Typically they run away from things they don't like, such as a farmer running away from bushes or a would-be doctor running away from herbs. See what you have the villager doing, check to see what his dislikes are, and most likely he's running away from that.

And bajantara, I've never had a villager who ran away from snakes... maybe your villager was eating a few too many mushrooms? LOL