Effect of valve position on parallel Pipeline

We have an HRSG as a part of GTG-HRSG package. It has two burner stages. The gas fed to it comes in at fixed Temperature and pressure.
It then bifurcates for each stage. Each stage pipeline has same Control Valves, Flowmeters and other instrument fittings.

The gas to first stage has to be varied across the entire day (Least at Noon, Max at Midnight) as the exhaust temperature of the GTG varies. The opening of the second stage remains the same throughout the day.

The issue here is that we have observed change in gas flow of the second stage as well during the day. The gas flow DECREASES during the DAY and INCREASES during the NIGHT.

I see no possible reason for this, perhaps I am missing out on something.