I have the same problem, 'cause some players play more minutes than others. maybe for his game shape, skills or because the Coach decided. The only way that I'm using now is only use the player for that position in a match. No matters what happen. The other one in the next match and the third in the Scrimmage.
By example, mi last scrimmage I only put four startup players.... an all of them, played the 48 minutes....