That happens to me too in my season often my opponents have the pitcher hitting, it hasnt happened to my team yet however. and today I was playing my Yankees season and I was playing the 05 ASG (Im a little behind the real life schedule but my yanks are like 83-3 right now) and jeter was voted the strating SS and tejada a backup, but the cpu put Tejada in as the starting dh for some reason.
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I can't even count the number of glitches in that game. Some of my favorites include the time I won the ASG as the NL in my franchise yet somehow the game decided that the AL won it. Or how most times pitchers who don't even pitch in the game get wins/saves. My rotation also resets itself after every game. I like the game but 2K Games really needs to fix this kind of shit for next year.
Anyway, I'm enjoying Madden and the new passing system as well. I'm 6-1 with my Bills franchise (on All-Pro), and this is mostly due to Willis McGahee and my defense carrying the team, which is pretty much like it is in real life.