Before too much hating goes on here, if you are supersimming, make sure that you go to supersim BEFORE you make the mass substitution...
i.e. i have found that if you go to mass subs, then return to the playcall screen and select supersim from there, it automatically puts your starters back in. However, if you go to supersim, THEN pause and go to mass subs, and then return DIRECTLY to supersim from the pause menu, your 2nd string should stay in