Are you using the Lahman DB or Spritze/Gambo? It sounds like you are using Lahman and selected "neutralized" stats when setting up the league? I was told not to do this although I'm not sure the reason.
However, if not using neutralized stats in a historical replay then the Rockies hitters and Safeco pitchers are always going to be far ahead of even their RL bloated stats, right?