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I really don't know if this means anything, but in Play Now mode the Skill is set to Custom, but Custom is not available in CCM. You can adjust the sliders, so maybe the All-Pro or All-Madden doesn't mean anything.
I think that adjustments to see test are:
Hum/ CPU
Run Block 54/52
Tackles 40/39
A couple of change I would like to consider for testing is too play in CCM instead of Play Now, as I am not sure if they play exactly the same (I think they do, but just to make sure). If you play a game run it back and switch teams (that way we can see if its the sliders or the match-up that generates the difference). Just my thoughts.
Hope everyone has a great Thanksgiving.