The position of an equilibrium is affected by many things. This means that the relative concentrations of reactant and products can differ. Although the rate of the forward reaction is the same as the rate of the reverse reaction, you can still start off with more ammonia. However, equilibria are affected by concentration.
Haber Process an Example of Keq
If there is more ammonia, the equilibrium will shift to try and make things equal again. This means the reverse reaction will speed up a bit, until the concentrations are where they want to be, and then it will return to a constant dynamic equilibrium - forward and reverse reactions being the same.