So I went through the steps last night. Everything seemed well. I filled all of the rosters with fictional players and then did a quick run through every team.
I did all of this in commissioner mode (I have 2 manager accounts, a commissioner and a St Louis Cards manager). The Cardinals did not receive an ML roster of players, all other teams did and all minor league teams received full rosters. No players for the ML Cardinals.
I am just going to try the whole thing over again, does anyone have any ideas?