It must be due to the limitation of calculating du/dt. If you are using all the default setting, you'll notice some warning message in the Command Window regarding step size.
There is no perfect way of calculating the theoretical du/dt in numerical simulation. Doing the du/dt first and then the integration is the problem. If you move the two integrators ahead of the du/dt block (right after the negative feedback summation block), you'll find that the results match perfectly.