A few things to note.
1. The Pulse Generator block outputs 1 for the first 500ns, then 0 for the second 500ns. It's not 0 first and then 1.
2. Sounds like you want to run your simulation at every 400ns, but the fact that your pulse generator is at period of 1000ns and 50% duty cycle. You have to run it at time step=100ns to hit 400ns, 500ns, 800ns ... Use fixed step discrete solver.
Could you try this? It should not be any problem or data discrepancy.
