I try 4-1-4-1 few times and lost always, my standard formation its 4-4-2c so I think in stronger like that.
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It has more to do with the orders. Maybe you did not use the best orders for 4-1-4-1 to counter 4-3-3, but you got the orders right for the 4-4-2 against 4-3-3. It depends also on what orders the opponent use.