In a way that's not really all that surprising. If a team is losing they are going to throw more often, and that results in more passing yards for the quarterback. If a team is winning then they are going to run more often, and that results in more rushing yards for the running back.
It's all due to the way the game clock is stopped or not stopped depending on what the previous play (completed pass or run) was. If the rules were that the game clock stopped (or kept going) regardless of what the previous type of play was, you wouldn't see this disparity. Similarly if football was like baseball, where instead of 60 minutes of play each team had nine possessions, the decisions on whether to pass or run in the second half would change dramatically.