I won Utopia cup playing 3-2 and I dont have any of the problems you are talking about. And having SB in your inside players is not a problem for this zone.
I also wonder if SB+OD combination (my center is a bit better than starting PG - who is a PF - in outside defense, one skill point, with his OD probably being half of what the opponent's JS was on two positions)
My guess is that your OD is not very good, so the zone doesnt work as intended.