An orifice/restriction/valve is never fully closed in Simscape. You'll always have a minimum area or opening fraction, aka leakage. This is by design and to avoid the change to the system of equations in the middle of a simulation. You just need to make the leakage small enough of the leakage (which is REAL in actual systems btw) doesn't matter for the main results you are studying.
The "closed" behavior you saw with the square wave is probably just a matter of scale of the y-axis.
What makes wonder though, is that your model seems to have the flow going from a reservoir through pipes and valves and back to the reservoir itself. I'm confused with where the driving pressure gradient comes from.
