WOW that is a large difference however, results for the same card will vary from system to system but, a 50% difference won't cover that. is that lack of performance for all games that you play?
have you looked to see if there is a difference in settings such as enabling tressFX - i understand that will take any nvidia card down to it's knees. you may want to consider playing a little "driver roulette" and try a few different drivers to see if you get anything from it.
aside from a software (settings and drivers) approach you ought to swap the card in the first slot if you can.
really it ought not make that much (~50%) of a difference but anything could be happening that is unexplainable.