Even with 2 identical systems the hardware is always going to be slightly different when it handles programs. Example is you can take 2 identical pc's and your able to overclock to x speed and not the other...

That aside. Are both running identical software? If not try just unloading everything but the game and see if the problem still happens... If it doesn't reload each app tell the problem happens could be the way 1 app takes over some processes.